From 1563efcc70d89db15021701b61508cedf9bcadc2 Mon Sep 17 00:00:00 2001
From: Suchita Lulla <suchitalulla@gmail.com>
Date: Wed, 27 Oct 2021 17:33:19 -0600
Subject: [PATCH 1/9] Core report functionality

---
 report/KCNQ2_coverage.bedgraph | 1763 +++++++++++++++++++
 report/axes.py                 |   41 +
 report/colors.py               |   37 +
 report/constraintview.py       |  286 ++++
 report/constraintview.yaml     |  110 ++
 report/expected_mut_counts.txt | 2899 ++++++++++++++++++++++++++++++++
 report/get_coords.py           |   99 ++
 report/glyphs.py               |  281 ++++
 report/map_coords.py           |   26 +
 report/named_colors.yaml       |   91 +
 report/observed_mut_counts.txt | 2899 ++++++++++++++++++++++++++++++++
 report/palettes.yaml           |    8 +
 report/plot.html               |   86 +
 report/project_coords.py       |  484 ++++++
 report/test.py                 |    2 +
 report/test1.html              |   86 +
 report/widget_callbacks.py     |  375 +++++
 17 files changed, 9573 insertions(+)
 create mode 100755 report/KCNQ2_coverage.bedgraph
 create mode 100755 report/axes.py
 create mode 100755 report/colors.py
 create mode 100755 report/constraintview.py
 create mode 100755 report/constraintview.yaml
 create mode 100755 report/expected_mut_counts.txt
 create mode 100755 report/get_coords.py
 create mode 100755 report/glyphs.py
 create mode 100755 report/map_coords.py
 create mode 100755 report/named_colors.yaml
 create mode 100755 report/observed_mut_counts.txt
 create mode 100755 report/palettes.yaml
 create mode 100644 report/plot.html
 create mode 100755 report/project_coords.py
 create mode 100755 report/test.py
 create mode 100644 report/test1.html
 create mode 100755 report/widget_callbacks.py

diff --git a/report/KCNQ2_coverage.bedgraph b/report/KCNQ2_coverage.bedgraph
new file mode 100755
index 0000000..61a8446
--- /dev/null
+++ b/report/KCNQ2_coverage.bedgraph
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diff --git a/report/axes.py b/report/axes.py
new file mode 100755
index 0000000..81b911f
--- /dev/null
+++ b/report/axes.py
@@ -0,0 +1,41 @@
+from bokeh.models import LinearAxis,Range1d
+
+def add_axis(plot, plot_params, axis_label, y_max, min_tick, max_tick, tick_precision, tick_scientific_notation, y_min=0, num_ticks=3, axis_position='right', visible=True):
+
+    ticks = [(max_tick-min_tick)/(num_ticks+1)*i+min_tick for i in range(num_ticks+2)]
+    ticks = list(map(lambda x: int(x) if int(x)==x else x , ticks)) #have to do this for overrides to work on ticks ending in .0
+    ticker_dict = {tick:str((y_max-y_min)/(num_ticks+1)*(idx)+y_min) for idx,tick in enumerate(ticks)}
+    #tick formatting
+    ticker_dict = format_ticks(ticker_dict, tick_precision, tick_scientific_notation)
+    plot.extra_y_ranges[axis_label] = Range1d(0,plot_params['plot_height'])
+    axis = LinearAxis(y_range_name=axis_label, axis_label=axis_label, ticker=ticks, major_label_overrides=ticker_dict, visible=visible)
+    plot.add_layout(axis, axis_position)
+    return axis
+
+def add_user_axis(plot, plot_params, user_line_params, axis_name, y_max, min_tick, max_tick, y_min=0, num_ticks=3, axis_position='right', visible=True):
+    axis_label = user_line_params[axis_name]['y_axis_label']
+    axis = add_axis(plot, plot_params, axis_label, y_max, min_tick, max_tick, user_line_params[axis_name]['tick_precision'], user_line_params[axis_name]['tick_scientific_notation'], y_min=y_min, num_ticks=num_ticks, axis_position=axis_position, visible=visible)
+    return axis
+
+def add_variant_axis(plot_params, variant_params, plot, axis_label, allele_vals, visible=True):
+    y_min = min(allele_vals)
+    y_max = max(allele_vals)
+    min_tick = plot_params['y0']+variant_params['min_lollipop_height']
+    max_tick = plot_params['plot_height']-variant_params['lollipop_radius']-variant_params['lollipop_line_width']
+    tick_precision = 2 #TODO
+    tick_scientific_notation = False
+    num_ticks = 3
+    axis_position = 'left'
+    visible = visible
+    axis = add_axis(plot, plot_params, axis_label, y_max, min_tick, max_tick, tick_precision, tick_scientific_notation, y_min=y_min, num_ticks=num_ticks, axis_position=axis_position, visible=visible)
+    return axis
+
+
+def format_ticks(ticker_dict, tick_precision, tick_scientific_notation):
+    for key in ticker_dict:
+        if int(float(ticker_dict[key])) == float(ticker_dict[key]): ticker_dict[key] = str(int(float(ticker_dict[key])))
+    for key in ticker_dict:
+        if tick_scientific_notation: format_precision = '.{}e'.format(tick_precision)
+        else: format_precision = '.{}f'.format(tick_precision)
+        ticker_dict = {key:format(float(value),format_precision) for (key,value) in ticker_dict.items()}
+    return ticker_dict
diff --git a/report/colors.py b/report/colors.py
new file mode 100755
index 0000000..4722856
--- /dev/null
+++ b/report/colors.py
@@ -0,0 +1,37 @@
+import numpy as np
+import random
+
+def lighten_hex_color(color, delta):
+    def limit(x):
+        if x > 255: return 255
+        if x < 0: return 0
+        return x
+
+    if '#' in color: color = color[1:]
+
+    r = hex(limit(int(color[:2], 16) + delta))[2:]
+    g = hex(limit(int(color[2:4], 16) + delta))[2:]
+    b = hex(limit(int(color[4:6], 16) + delta))[2:]
+
+    new_color = '#{}{}{}'.format(r, g, b)
+    return new_color
+
+def color_variants(plot_params, variant_params, variant_ls):
+    #colors = [variant_params['variant_severity_colors'][v['severity']] for v in variant_ls]
+    for v in variant_ls:
+        #v['color'] = variant_params['variant_severity_colors'][v['severity']]
+        if v['severity']: v['color'] = variant_params['variant_severity_colors'][v['severity']]
+        else: v['color'] = plot_params['glyph_colors']['variant']
+
+
+def color_boxes(plot_params, user_track_params, track_name, boxes):
+    IDs = np.unique([b['ID'] for b in boxes])
+    color_dict = {ID: random.choice(np.unique(plot_params['track_colors'])) for ID in IDs}
+
+    try:
+        for (ID, color) in user_track_params[track_name]['colors'].items():
+            color_dict[ID] = color
+    except: pass
+
+    for idx in range(len(boxes)):
+        boxes[idx]['color'] = color_dict[boxes[idx]['ID']]
\ No newline at end of file
diff --git a/report/constraintview.py b/report/constraintview.py
new file mode 100755
index 0000000..78c540f
--- /dev/null
+++ b/report/constraintview.py
@@ -0,0 +1,286 @@
+from get_coords import get_variants,get_line,get_track
+from map_coords import map_line
+from colors import color_boxes, color_variants
+from axes import add_user_axis,add_variant_axis
+from glyphs import add_intron_glyph, add_exon_glyph, add_variant_glyph, add_UTR_glyph, add_track_glyph, add_multi_line_glyph
+from widget_callbacks import add_checkbox,add_user_tracks_checkbox,add_user_lines_checkbox,add_smoothing_slider,add_legend,add_linear_log_scale,add_exon_zoom
+import project_coords
+import gffutils
+import numpy as np
+import argparse
+from bokeh.plotting import figure, output_file, save
+from bokeh.layouts import column, row, gridplot
+from bokeh.models import ColumnDataSource, Range1d, HoverTool, LabelSet
+#import tabix
+import yaml
+from yaml.loader import SafeLoader
+
+def get_gene_feature(gff_db, gene_name):
+    #get ID from name
+    for f in gff_db.all_features(featuretype='gene'):
+        try:
+            if gene_name in f['Name'][0]: return f
+        except: continue
+    raise ValueError('No gene with name {}'.format(gene_name))
+    
+def get_transcript_dict(plot_params, gff_db, gene_feature, transcript_IDs):
+    chr_num = gene_feature.seqid
+    print(chr_num)
+    transcript_dict = {}
+
+    #get all exons and flatten
+    if 'flattened-exons' in transcript_IDs or transcript_IDs=='all':
+        exons_all = gff_db.children(gene_feature, featuretype='exon')
+        exons_all = [{'start': e.start, 'end': e.end} for e in exons_all]
+        exons_all = project_coords.flatten_exons(exons_all)
+        transcript_dict['flattened-exons'] = dict(ID='flattened_exons', chr_num=chr_num, exons=exons_all,
+                                                  direction='', UTRs=[])    
+        
+    def get_UTRs(transcript):
+        if not plot_params['plot_UTRs']: return []
+        UTRs = []
+        for f in ['five_prime_UTR', 'three_prime_UTR']:
+            try:
+                UTR = list(gff_db.children(transcript, featuretype=f))
+                if len(UTR) > 1: 
+                    print('Warning: transcript {} has {} {} annotations; using first annotation.'.format(tname, len(UTR), featuretype))
+                UTR_dict = {'featuretype': f, 'start': UTR[0].start, 'end': UTR[0].end}
+                UTRs.append(UTR_dict)
+            except: continue 
+        return UTRs
+                
+    #indiv mRNAs
+    transcripts = list(gff_db.children(gene_feature, featuretype='mRNA'))
+    if transcript_IDs != 'all':
+        for ID in transcript_IDs:
+            if ID not in [t['Name'][0] for t in transcripts]: print('No such transcript {}; skipping'.format(ID))
+        transcripts = [t for t in transcripts if t['Name'][0] in transcript_IDs]
+        #print([t['ID'] for t in transcripts])
+
+    for t in transcripts:
+        exons = list(gff_db.children(t, featuretype='exon'))
+        exon_coords = [{'start': e.start, 'end': e.end, 'compact_start': -1, 'compact_end': -1} for e in exons]
+        direction = t.strand if plot_params['plot_direction'] else ''
+        tname = t['Name'][0]
+        UTRs = get_UTRs(t)
+        transcript_dict[tname] = dict(ID=t['ID'], chr_num=chr_num, exons=exon_coords, direction=direction, 
+                                UTRs=UTRs)
+    return transcript_dict
+
+def gff_to_db(gff_path,output_name):
+    try:
+        db = gffutils.FeatureDB(gff_path, keep_order=True)
+    except:
+        gffutils.create_db(gff_path, dbfn=output_name, force=True, keep_order=True, merge_strategy='merge', sort_attribute_values=True)
+        db = gffutils.FeatureDB(gff_path, keep_order=True)
+    return db
+
+def constraint_view_plot(plot_params, variant_params, user_line_params, transcript_dict, glyph_dict, axes, variant_ls, user_tracks, user_track_glyphs, user_lines, user_line_glyphs, title=''):
+    project_coords.adjust_coordinates(transcript_dict['exons'], intron_size=plot_params['intron_size'])
+    plot_height = plot_params['plot_height']    
+    plot = figure(title=title, plot_width=1500, tools='tap,box_zoom,xpan,reset', plot_height=plot_height,min_border=0,#, toolbar_location=None,
+               x_range=Range1d(0, transcript_dict['exons'][-1]['compact_end']), y_range=Range1d(0,plot_height), background_fill_color='white')
+    
+    plot.grid.grid_line_color = None
+    plot.toolbar.active_drag = None
+    plot.yaxis[0].visible = False
+    
+    ###VARIANTS###
+    if variant_ls:
+        project_coords.map_point(variant_ls, transcript_dict['exons'])
+        ray_glyph,circle_glyph,allele_counts,allele_frequencies = add_variant_glyph(plot_params, variant_params, plot, variant_ls)
+        if ray_glyph and circle_glyph:
+            tooltips_variations = [('Position (compact)', '@x'), ('Position (chr)', '@pos'), 
+                                   ('Allele count', '@allele_counts'), ('Allele number', '@allele_numbers'), ('Allele frequency', '@allele_frequencies'), 
+                                   ('Change', '@ref > @alt'), ('VEP Annotation', '@ann'), ('Severity', '@sev')]
+            plot.add_tools(HoverTool(tooltips=tooltips_variations, renderers=[circle_glyph,ray_glyph], point_policy='follow_mouse', attachment='below'))
+        glyph_dict['Variant'].extend([ray_glyph,circle_glyph])
+        
+        axes['count'].append(add_variant_axis(plot_params, variant_params, plot, 'Allele count', allele_counts, visible=True))
+        axes['allele_frequency'].append(add_variant_axis(plot_params, variant_params, plot, 'Allele frequency',allele_frequencies, visible=False))
+
+    tooltips_features = [('Type','@feat_type'), ('Start (compact)', '@adj_start'), ('End (compact)', '@adj_end'), 
+                      ('Start (chr)', '@true_start'), ('End (chr)', '@true_end'), ('Length', '@true_len')]
+
+    ###INTRONS###
+    introns = project_coords.get_introns_from_exons(transcript_dict['exons'])
+    introns_glyph = add_intron_glyph(plot_params, plot, introns)
+    plot.add_tools(HoverTool(tooltips=tooltips_features, renderers=[introns_glyph], point_policy='follow_mouse', attachment='below'))    
+    
+    ###EXONS###
+    exons_glyph,arrow_glyph = add_exon_glyph(plot_params, plot, transcript_dict['exons'], transcript_dict['direction'])
+    plot.add_tools(HoverTool(tooltips=tooltips_features, renderers=[exons_glyph], point_policy='follow_mouse', attachment='below'))
+    
+    glyph_dict['Direction'].append(arrow_glyph)
+    glyph_dict['exon'].append(exons_glyph)
+
+    ###UTRs###
+    project_coords.map_box(transcript_dict['UTRs'], transcript_dict['exons'])
+    UTR_glyph = add_UTR_glyph(plot_params, plot, transcript_dict['UTRs'])
+    plot.add_tools(HoverTool(tooltips=tooltips_features, renderers=[UTR_glyph], point_policy='follow_mouse', attachment='below'))    
+    glyph_dict['UTRs'].append(UTR_glyph)
+
+    ###USER TRACKS###
+    h = plot_params['track_height']
+
+    for idx,track_name in enumerate(user_tracks):
+        project_coords.map_box(user_tracks[track_name], transcript_dict['exons'])
+
+        tooltips_tracks = [('Name','@track_names'), ('Start (adjusted)', '@adj_start'), ('End (adjusted)', '@adj_end'), 
+                          ('Start (true)', '@true_start'), ('End (true)', '@true_end'), ('Length', '@true_len')]
+        
+        y = ((h*1.5)*(len(user_tracks) - idx - 1)+(h))
+        track_glyph = add_track_glyph(plot, user_tracks[track_name], h*0.9, y)
+        plot.add_tools(HoverTool(tooltips=tooltips_tracks, renderers=[track_glyph], point_policy='follow_mouse', attachment='below'))
+        user_track_glyphs[track_name].append(track_glyph)
+        cs = ColumnDataSource(dict(x=[0], y=[(h*1.5)*(len(user_tracks) - idx - 1)], text=[list(user_tracks.keys())[idx]]))
+        label = LabelSet(source=cs, x='x', y='y', text='text',text_font_size='{}px'.format(plot_params['track_height']),
+                    text_align='left')
+        plot.add_layout(label)
+        user_track_glyphs[track_name].append(label)
+        
+    ###user lines###
+    for idx,axis_name in enumerate(user_line_params):
+        all_xs = []
+        all_ys = []
+        for line in user_line_params[axis_name]['lines']:
+                xs_ls,ys_ls = map_line(user_lines[axis_name][line], transcript_dict['exons'])
+                all_xs.append(xs_ls)
+                all_ys.append(ys_ls)
+        y_max = max([item for sublist in list(np.array(all_ys,dtype=object).flat) for item in sublist])
+        
+        for idx,line in enumerate(user_line_params[axis_name]['lines']):
+            line_params=user_line_params[axis_name]['lines'][line]
+            line_glyph = add_multi_line_glyph(plot_params, plot, all_xs[idx], all_ys[idx], max_y=y_max, y0=plot_params['y0'], fill_area=line_params['fill_area'], line_color=line_params['color'], line_alpha=line_params['alpha'])
+            line_glyph.level = 'underlay'
+            user_line_glyphs[axis_name].append(line_glyph)
+            
+        add_user_axis(plot, plot_params, user_line_params, axis_name, y_max, plot_params['y0'], plot_params['plot_height'], y_min=0, num_ticks=3, axis_position='right', visible=True)
+
+    return plot,glyph_dict
+
+def parse_args():
+    parser = argparse.ArgumentParser(description='constraintview')
+    parser.add_argument('config_file', help='must be .yaml; sample config file can be found at xyz')
+    parser.add_argument('transcripts', help='transcripts to plot, can be [... str] or all')
+    parser.add_argument('-o', '--output', required=False, help='output filepath')
+    args = parser.parse_args()
+
+    ###CONFIG###
+    config_file = args.config_file
+    # TODO what to do if config file doesn't have required params?
+    if config_file[-5:] != '.yaml': raise ValueError('configuration file must be .yaml')
+    with open(config_file) as f:
+        params = list(yaml.load_all(f, Loader=SafeLoader))
+        plot_params = params[0]
+        variant_params = params[1]
+        user_track_params = params[2]
+        user_line_params = params[3]
+        plot_params['transcript_height'] = 20 + len(user_track_params) * plot_params['track_height'] * 1.5
+        plot_params['y0'] = plot_params['transcript_height'] + plot_params['exon_height'] / 2  # "0" for line plots
+
+    ###COLORS###
+    with open('named_colors.yaml') as f:
+        named_colors = list(yaml.load_all(f, Loader=SafeLoader))[0]
+
+    ###GLYPH COLORS###
+    for glyph_type in plot_params['glyph_colors']:
+        color = plot_params['glyph_colors'][glyph_type]
+        if color[0] != "#": plot_params['glyph_colors'][glyph_type] = named_colors[color]
+
+    ###TRACKS###
+    for track_name in user_track_params:
+        track_db = gff_to_db(user_track_params[track_name]['gtf_path'], user_track_params[track_name]['gtf_path'] + '.db')
+        user_track_params[track_name]['db'] = track_db
+    with open('palettes.yaml') as f:
+        palettes = list(yaml.load_all(f, Loader=SafeLoader))[0]
+    track_colors = [named_colors[c] for c in palettes[plot_params['track_palette']]]
+    plot_params['track_colors'] = track_colors
+
+    ###TRANSCRIPTS###
+    transcript_IDs = args.transcripts
+    if transcript_IDs != 'all':
+        transcript_IDs = transcript_IDs.strip('[').strip(']').split(',')
+        transcript_IDs = [t.strip('\'') for t in transcript_IDs]
+
+    ###OUTPUT###
+    if args.output: output = args.output + '.html' if args.output[-5:] != '.html' else args.output
+    else: output = 'plot.html'
+    return plot_params,variant_params,user_track_params,user_line_params,transcript_IDs,output
+
+def constraint_view():
+    plot_params, variant_params, user_track_params, user_line_params, transcript_IDs, output = parse_args()
+
+    # 'test.db' to make sure .db does not get overwritten during development    
+    gff_db = gff_to_db(plot_params['gff_path'],plot_params['gff_path']+'test.db')
+    
+    gene_feature = get_gene_feature(gff_db, plot_params['gene_name'])
+
+    if transcript_IDs == 'transcript_names':
+        transcripts = get_transcript_dict(plot_params, gff_db, gene_feature, 'all')
+        print(list(transcripts.keys()))
+        exit()
+
+    transcripts = get_transcript_dict(plot_params, gff_db, gene_feature, transcript_IDs)
+    transcript_IDs = list(transcripts.keys()) #if 'all', transcript_IDs will become list of transcript names; if nonexistent IDs they are removed
+    
+    variant_ls = get_variants(plot_params['variant_path']) if variant_params['plot_variants'] else []
+    color_variants(plot_params, variant_params, variant_ls)
+    user_tracks = {track_name: get_track(user_track_params, track_name) for track_name in user_track_params}
+    for track_name in user_tracks: color_boxes(plot_params, user_track_params, track_name, user_tracks[track_name])
+    user_lines = {axis_name:{} for axis_name in user_line_params}
+    for axis_name in user_line_params:
+        for line_name in user_line_params[axis_name]['lines']:
+            user_lines[axis_name][line_name] = get_line(user_line_params[axis_name]['lines'][line_name]['filepath'])
+    
+    plot_ls = []
+    glyph_dict = dict(exon=[],UTRs=[],Variant=[],Direction=[])
+    user_track_glyphs = {track_name:[] for track_name in user_track_params}
+    user_line_glyphs = {line_name:[] for line_name in user_line_params}
+    axes = dict(count=[],allele_frequency=[])
+    for line_name in user_line_params:
+        axes[line_name] = []
+    
+    for idx,ID in enumerate(transcript_IDs):
+        title = 'gene={}; transcript={}/{}'.format(plot_params['gene_name'], ID, transcripts[ID]['ID'])
+        if transcripts[ID]['direction']: title += ' ({})'.format(transcripts[ID]['direction'])
+        plot,glyph_dict = constraint_view_plot(plot_params, variant_params, user_line_params, transcripts[ID], glyph_dict, axes, variant_ls, user_tracks, user_track_glyphs, user_lines, user_line_glyphs, title=title)
+        plot_ls.append(plot)
+    
+    legend = add_legend(user_line_params)
+    add_exon_zoom(plot_ls,glyph_dict)
+    checkbox = add_checkbox(plot_ls,axes,glyph_dict,plot_params, variant_params)
+    user_tracks_checkbox = add_user_tracks_checkbox(plot_ls,axes,user_track_glyphs,glyph_dict['Direction'],plot_params)
+    
+    user_line_checkboxes=[] #one checkbox per user line, so that they can be lined up with sliders
+    for axis in user_line_params:
+        user_line_checkbox = add_user_lines_checkbox(plot_ls, axes[axis], user_line_glyphs[axis], axis)
+        user_line_checkboxes.append(user_line_checkbox)
+    
+    if variant_params['plot_variants']:
+        div_type,radio_group_type,div_scale,radio_group_scale = add_linear_log_scale(axes, glyph_dict)
+    
+    sliders = []
+    for axis_name in user_line_params:
+        if user_line_params[axis_name]['smoothing_slider']:
+            fill_area_ls = [user_line_params[axis_name]['lines'][line]['fill_area'] for line in user_line_params[axis_name]['lines']]*len(plot_ls)
+            sliders.append(add_smoothing_slider(user_line_glyphs[axis_name], fill_area_ls, title='{} smoothing'.format(axis_name)))
+        else:
+            sliders.append(None)
+    
+    if variant_params['plot_variants']:
+        grid1 = [[checkbox, user_tracks_checkbox],[div_type, div_scale],[radio_group_type, radio_group_scale]] 
+    else: grid1 = [[checkbox, user_tracks_checkbox]]
+    
+    lines = list(zip(user_line_checkboxes,sliders))
+    for tup in lines: grid1.append(tup)
+    grid1.append([legend])
+    grid = gridplot(grid1, toolbar_location=None)
+    
+    output_file(output)
+    save(column([grid]+plot_ls))
+
+#t0 = time.time()
+constraint_view()
+#t1 = time.time()
+#print(t1-t0)
\ No newline at end of file
diff --git a/report/constraintview.yaml b/report/constraintview.yaml
new file mode 100755
index 0000000..51230f2
--- /dev/null
+++ b/report/constraintview.yaml
@@ -0,0 +1,110 @@
+---
+###Data params
+###LOCAL PATHS
+#gff_path: 'Homo_sapiens.GRCh38.104.gff3.db' #if not database file, database will be created for you
+#variant_path: 'gnomAD_v3.1.1_KCNQ2.csv'
+#variant_path: 'gnomad_v3_variants.bed'
+###REMOTE PATHS
+gff_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/Homo_sapiens.GRCh38.104.gff3.db'
+variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomAD_v3.1.1_ENSG00000075043_2021_09_16_16_02_28.csv'
+#variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomad.exomes.r2.1.1.sites.20.vcf.bgz'
+model_path : '/uufs/chpc.utah.edu/common/HIPAA/u6038618/constraint-tools/test-model/model-new-modified.json'
+####Plot params
+gene_name: 'KCNQ2'
+
+plot_height: 200
+plot_width: 1500
+track_height: 10
+exon_height: 16 #must be even
+intron_size: 20
+
+plot_UTRs: True
+plot_direction: True
+
+glyph_colors:
+    intron: 'gray 11'
+    exon: 'davys gray'
+    arrow: '#252525'
+    UTR: '#969696'
+    variant: 'charcoal' #default lollipop color if no severity information
+
+track_palette: 'blues' #palette to draw random track colors from; can be any one palette in palettes.yaml
+...
+---
+#variants
+plot_variants: True
+min_lollipop_height: 15
+lollipop_radius: 5
+lollipop_line_width: 2
+variant_severity_colors:
+    LOW: '#80b918'
+    #LOW: 'apple green'
+    MODERATE: '#f6aa1c'
+    HIGH: '#e01e37'
+    MODIFIER: '#778da9'
+...
+
+---
+###User defined tracks:
+
+domains:
+    #LOCAL
+    #gtf_path: 'pfam.sorted.gtf.db' #must be .gff, .gtf, .gff.db, or .gtf.db; if not database, database will be created for you
+    #REMOTE
+    gtf_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/pfam.sorted.gtf.db'
+    seqid: chr20
+    colors: #leave empty to color all randomly
+        Ion_trans: '#f3722c' #color these boxes as specified, any unspecified boxes colored randomly
+        KCNQC3-Ank-G_bd: '#A09BE7'
+
+domains2:
+    #LOCAL
+    #gtf_path: 'pfam.sorted.gtf.db' #must be .gff, .gtf, .gff.db, or .gtf.db
+    seqid: chr20
+    #REMOTE
+    gtf_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/pfam.sorted.gtf.db'
+#    colors: #leave empty to color all randomly
+
+domains3:
+    #LOCAL
+    #gtf_path: 'pfam.sorted.gtf.db' #must be .gff, .gtf, .gff.db, or .gtf.db
+    seqid: chr20
+    #REMOTE
+    gtf_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/pfam.sorted.gtf.db'
+...
+---
+###User defined axes:
+
+Coverage:
+    #axis params
+    y_axis_label: 'Sequencing Coverage (30x)'
+    num_ticks: 3
+    tick_precision: 2 #number of decimal places
+    tick_scientific_notation: False #format ticks to scientific notation
+    smoothing_slider: False
+    lines:
+        Coverage:
+            #line params
+            filepath: 'KCNQ2_coverage.bedgraph'
+            color: '#00916E'
+            alpha: 0.5
+            fill_area: True
+
+Mutation counts:
+    y_axis_label: 'Number of mutations'
+    num_ticks: 3
+    tick_precision: 4 #
+    tick_scientific_notation: False
+    smoothing_slider: True
+    lines:
+        Expected mutation counts: 
+            filepath: 'expected_mut_counts.txt'
+            color: '#f26419'
+            alpha: 1
+            fill_area: False
+        Observed mutation counts:
+            filepath: 'observed_mut_counts.txt'
+            #filepath: 'observed_mut_counts_two_fields.txt'
+            color: '#19a7f2'
+            alpha: 1
+            fill_area: False
diff --git a/report/expected_mut_counts.txt b/report/expected_mut_counts.txt
new file mode 100755
index 0000000..c418e72
--- /dev/null
+++ b/report/expected_mut_counts.txt
@@ -0,0 +1,2899 @@
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diff --git a/report/get_coords.py b/report/get_coords.py
new file mode 100755
index 0000000..f52595e
--- /dev/null
+++ b/report/get_coords.py
@@ -0,0 +1,99 @@
+import csv
+
+def variant_type(annotation):
+    if annotation in ['synonymous_variant']:
+        return 'LOW'
+    if annotation in ['missense_variant', 'inframe_deletion', 'inframe_insertion','stop_lost',]:
+        return 'MODERATE'
+    if annotation in ['splice_acceptor_variant','frameshift_variant','splice_donor_variant','stop_gained',]:
+        return 'HIGH'
+    if annotation in ['3_prime_UTR_variant', '5_prime_UTR_variant', 'splice_region_variant','intron_variant',]:
+        return 'MODIFIER'
+    #print('No classification for variant type {}; classified as "other"'.format(annotation))
+    return 'MODIFIER'
+
+def get_variants(filepath):
+    
+    def get_variants_vcf(vcf_path):
+        variant_ls = []
+        import tabix #putting import here for now because it doesn't work on local machine
+        tb = tabix.open(vcf_path)
+        for idx,r in enumerate(tb.query('20',62037947,62137947)): #TODO don't hardcode params
+            variant_ls.append(dict(pos=int(r[1])+1400000, compact_pos=-1, ref=r[3], alt=r[4], #adding 1.4m bc this vcf is on old build
+                              annotation=r[7].split(';')[-1].split('|')[1], severity=r[7].split(';')[-1].split('|')[2],
+                              allele_count=int(r[7].split(';')[0].split('=')[1]),
+                              allele_number=int(r[7].split(';')[1].split('=')[1]),
+                              allele_frequency=float(r[7].split(';')[2].split('=')[1])))
+        return variant_ls
+
+    def get_variants_csv(csv_path):
+        variant_ls = []
+        with open(csv_path, newline='') as csvfile:
+            reader = csv.reader(csvfile)
+            next(reader) #skip header
+            for row in reader:
+                variant_dict = dict(pos=int(row[1]), compact_pos=-1, ref=row[3], alt=row[4], 
+                               annotation=row[12], severity=variant_type(row[12]), 
+                               allele_count=int(row[16]), allele_number=int(row[17]), allele_frequency=float(row[18]))
+                variant_ls.append(variant_dict)
+        variant_ls = list({v['pos']:v for v in variant_ls}.values()) #remove duplicate dicts
+        return variant_ls
+
+    def get_variants_bed(bed_path):
+        #variant_ls = []
+        #f = open(bed_path, 'r')
+        #with open(bed_path) as bedfile:
+            #print('a')
+            #print(bedfile.readlines()[:10])
+        #  #x = bedfile.readlines()
+
+
+        return []
+    
+    if filepath.split('.')[-2] == 'vcf':
+        variant_ls = get_variants_vcf(filepath)
+    
+    elif filepath.split('.')[-1] == 'csv':
+        variant_ls = get_variants_csv(filepath)
+
+    elif filepath.split('.')[-1] == 'bed': #universal format
+        variant_ls = get_variants_bed(filepath)
+        
+    else: raise ValueError('Invalid filepath: {}'.format(filepath))
+
+    return variant_ls
+
+def get_line(filepath,chr_num=-1):
+    fi = open(filepath,'r')
+    line_coords = [line.strip().split('\t') for line in fi.readlines()]
+    
+    #boxes: <chr>\t<start>\t<end>\t<y>
+    if filepath.split('.')[-1] == 'bedgraph' or len(line_coords[0]) == 4:
+        line_coords = [{'chrom': int(chrom),'start': int(start), 'end': int(end), 'y': float(y)} for (chrom, start, end, y) in line_coords]
+        if chr_num >= 0: coords = [coord for coord in line_coords if coord['chrom']==chr_num]
+            
+    elif filepath.split('.')[-1] == 'txt':
+        if len(line_coords[0]) == 3:
+            line_coords = [{'chrom': chrom, 'pos': float(x), 'y': float(y)} for (chrom, x, y) in line_coords]
+            if chr_num >= 0: coords = [coord for coord in line_coords if coord['chrom']==chr_num]
+        elif len(line_coords[0]) == 2:
+            line_coords = [{'chrom': -1, 'pos': float(x), 'y': float(y)} for (x, y) in line_coords]
+        else:
+            raise ValueError('Invalid file format')
+
+    fi.close()
+    return line_coords
+
+
+def get_track(user_track_params, track_name, strand='-'):
+    boxes = []
+    db = user_track_params[track_name]['db']
+    seqid = user_track_params[track_name]['seqid']
+    for s in list(db.region(seqid=seqid, featuretype='exon', strand=strand)):  # [::-1]:
+        box_dict = dict(ID=s['gene_id'][0], start=s.start, end=s.end, compact_start=-1,
+                        compact_end=-1)  # more than one gene name?
+        boxes.append(box_dict)
+
+    return boxes
+
+
diff --git a/report/glyphs.py b/report/glyphs.py
new file mode 100755
index 0000000..c910a0d
--- /dev/null
+++ b/report/glyphs.py
@@ -0,0 +1,281 @@
+import numpy as np
+from bokeh.models import ColumnDataSource, Rect, Segment, Circle, MultiPolygons
+from colors import lighten_hex_color
+
+
+#param feature: (int, int); start and end of feature
+#return center: int; center point of feature
+def center_feature(feature):
+    center = feature[0] + (feature[1] - feature[0])/2
+    return center
+
+def add_exon_glyph(plot_params, plot, exons, direction):
+    features_original = [(exon['start'], exon['end']) for exon in exons]
+    features_compact = [(exon['compact_start'], exon['compact_end']) for exon in exons]
+
+    x = [center_feature(f) for f in features_compact]
+    y = [plot_params['transcript_height'] for f in features_compact]
+    w = [end - start for (start, end) in features_compact]
+    h = [plot_params['exon_height'] - 4 for f in features_compact]
+
+    # METADATA
+    feat_type = ['Exon' for f in features_compact]
+    adj_start = [start for (start, end) in features_compact]
+    adj_end = [end for (start, end) in features_compact]
+    true_start = [start for (start, end) in features_original]
+    true_end = [end for (start, end) in features_original]
+    true_len = [end - start + 1 for (start, end) in features_original]  # +1 for 1 indexed coords
+
+    exon_source = ColumnDataSource(dict(x=x, y=y, w=w, h=h,
+                                        feat_type=feat_type,
+                                        adj_start=adj_start, adj_end=adj_end,
+                                        true_len=true_len, true_start=true_start, true_end=true_end))
+
+    color = plot_params['glyph_colors']['exon']
+    hover_color = lighten_hex_color(color, 20)
+
+    exon_glyph = Rect(x='x', y='y', width='w', height='h', height_units='screen', fill_color=color, line_color=color)
+    hover_glyph = Rect(x='x', y='y', width='hover_w', height='hover_h', height_units='screen', fill_color=hover_color,
+                       line_color=hover_color)
+
+    if direction == '':
+        exon_glyph = plot.add_glyph(exon_source, exon_glyph, hover_glyph=hover_glyph)
+        return exon_glyph, None
+
+    # ADD ARROWS#
+    def adjust_arrow_coords(coords, direction):
+        ret = [j * (adj_end[i] - adj_start[i]) / 100 for j in coords]
+        while (max(ret) - min(ret)) / plot_params['plot_width'] > 0.01:
+            ret = [r * .9 for r in ret]
+
+        if direction == '-': ret = [-r for r in ret]
+        return [r + x[i] for r in ret]
+
+    xs_dict = []
+    for i in range(len(features_compact)):
+        xs_dict.append([{'exterior': adjust_arrow_coords([-20, -20, 0, 0], direction), 'holes': []}])
+        xs_dict.append([{'exterior': adjust_arrow_coords([0, 0, 20], direction), 'holes': []}])
+
+    ys_dict = []
+    for i in range(len(features_compact)):
+        ys_dict.append([{'exterior': [plot_params['transcript_height'] - plot_params['exon_height'] / 5,
+                                      plot_params['transcript_height'] + plot_params['exon_height'] / 5,
+                                      plot_params['transcript_height'] + plot_params['exon_height'] / 5,
+                                      plot_params['transcript_height'] - plot_params['exon_height'] / 5],
+                         'holes': []}])  # rect: prev [9, 11, 11, 9]
+        ys_dict.append([{'exterior': [plot_params['transcript_height'] - plot_params['exon_height'] / 2,
+                                      plot_params['transcript_height'] + plot_params['exon_height'] / 2,
+                                      plot_params['transcript_height']], 'holes': []}])  # triangle: prev [7,13,10]
+
+    xs = [[[p['exterior'], *p['holes']] for p in mp] for mp in xs_dict]
+
+    ys = [[[p['exterior'], *p['holes']] for p in mp] for mp in ys_dict]
+
+    color = plot_params['glyph_colors']['arrow']
+
+    arrow_source = ColumnDataSource(dict(x=xs, y=ys, fill_alpha=[1 for i in features_compact] * 2,
+                                         direction=[direction for i in features_compact] * 2))
+    arrow_glyph = plot.multi_polygons(source=arrow_source, xs='x', ys='y', fill_color=color, line_color=color,
+                                      fill_alpha='fill_alpha', line_alpha=0)
+    arrow_glyph.level = 'overlay'
+    arrow_glyph.nonselection_glyph = None
+
+    exon_glyph = plot.add_glyph(exon_source, exon_glyph, hover_glyph=hover_glyph, nonselection_glyph=None)
+
+    return exon_glyph, arrow_glyph
+
+def add_intron_glyph(plot_params, plot, introns, fill_alpha=1, width=14):
+    features_original = [(intron['start'], intron['end']) for intron in introns]
+    features_compact = [(intron['compact_start'], intron['compact_end']) for intron in introns]
+    x = [center_feature(f) for f in features_compact]
+    y = [plot_params['transcript_height'] for f in features_compact]  # prev 10
+    w = [plot_params['intron_size'] * 2 for f in features_compact]  # avoid white spaces
+    h = [plot_params['exon_height'] / 2 for f in features_compact]
+
+    ###METADATA
+    feat_type = ['Intron' for f in features_compact]
+    adj_start = [start for (start, end) in features_compact]
+    adj_end = [end for (start, end) in features_compact]
+    true_start = [start for (start, end) in features_original]
+    true_end = [end for (start, end) in features_original]
+    true_len = [end - start + 1 for (start, end) in features_original]  # +1 for 1 indexed coords
+    ###
+
+    source = ColumnDataSource(dict(x=x, y=y, w=w, h=h,
+                                   feat_type=feat_type,
+                                   adj_start=adj_start, adj_end=adj_end,
+                                   true_len=true_len, true_start=true_start, true_end=true_end))
+
+    color = plot_params['glyph_colors']['intron']
+    hover_color = lighten_hex_color(color, 50)
+
+    glyph = Rect(x='x', y='y', width='w', height='h', height_units='screen', fill_color=color, fill_alpha=fill_alpha,
+                 line_color=color)
+    hover_glyph = Rect(x='x', y='y', width='w', height='h', height_units='screen', fill_color=hover_color,
+                       fill_alpha=fill_alpha, line_color=hover_color)
+
+    return plot.add_glyph(source, glyph, hover_glyph=hover_glyph)
+
+
+def add_UTR_glyph(plot_params, plot, UTRs, fill_alpha=0.4):
+    features_original = [(UTR['start'], UTR['end']) for UTR in UTRs]
+    features_compact = [(UTR['compact_start'], UTR['compact_end']) for UTR in UTRs]
+    feat_type = [UTR['featuretype'] for UTR in UTRs]
+    x = [center_feature(f) for f in features_compact]
+    y = [plot_params['transcript_height'] for f in features_compact]  # prev 10
+    w = [end - start for (start, end) in features_compact]
+    h = [plot_params['exon_height'] - 4 for f in features_compact]
+
+    # metadata
+    adj_start = [start for (start, end) in features_compact]
+    adj_end = [end for (start, end) in features_compact]
+    true_start = [start for (start, end) in features_original]
+    true_end = [end for (start, end) in features_original]
+    true_len = [end - start + 1 for (start, end) in features_original]  # +1 for 1 indexed coords
+
+    source = ColumnDataSource(dict(x=x, y=y, w=w, h=h,
+                                   feat_type=feat_type,
+                                   adj_start=adj_start, adj_end=adj_end,
+                                   true_len=true_len, true_start=true_start, true_end=true_end))
+
+    color = plot_params['glyph_colors']['UTR']
+    hover_color = lighten_hex_color(color, 40)
+
+    glyph = Rect(x='x', y='y', width='w', height='h', height_units='screen', fill_color=color, fill_alpha=fill_alpha,
+                 line_color=color)
+    hover_glyph = Rect(x='x', y='y', width='w', height='h', height_units='screen', fill_color=hover_color,
+                       fill_alpha=fill_alpha, line_color=hover_color)
+
+    return plot.add_glyph(source, glyph, hover_glyph=hover_glyph)
+
+
+def add_variant_glyph(plot_params, variant_params, plot, variant_ls, height=9, radius=5,
+                      line_width=2):  # height prev 18
+    variant_ls = [v for v in variant_ls if v['compact_pos'] >= 0]
+    N = len(variant_ls)
+    if N == 0: return None, None, 0, 0
+    allele_counts = [v['allele_count'] for v in variant_ls]
+    allele_numbers = [v['allele_number'] for v in variant_ls]
+    allele_frequencies = [v['allele_frequency'] for v in variant_ls]
+    x = [v['compact_pos'] for v in variant_ls]
+    y0s = [plot_params['y0'] - plot_params['exon_height'] / 2] * N
+
+    def get_y1(fn, ls):
+        ls_fn = [fn(x) for x in ls]
+        for idx, x in enumerate(ls_fn):
+            if x < 0: raise ValueError('Lollipop height cannot be negative')
+        y1_circle = [c * (plot_params['plot_height'] - plot_params['y0'] - variant_params[
+            'min_lollipop_height'] - radius - line_width - 2) / max([c for c in ls_fn]) + plot_params['y0'] +
+                     variant_params['min_lollipop_height'] for c in ls_fn]
+        y1_segment = [y - radius for y in y1_circle]
+        return y1_circle, y1_segment
+
+    y1_ci_li_ct, y1_sg_li_ct = get_y1(lambda x: x, allele_counts)
+    y1_ci_lg_ct, y1_sg_lg_ct = get_y1(lambda x: np.log10(x) if x > 0 else 0, allele_counts)
+    y1_ci_li_fr, y1_sg_li_fr = get_y1(lambda x: x, allele_frequencies)
+    y1_ci_lg_fr, y1_sg_lg_fr = get_y1(lambda x: -np.log10(x) if x > 0 else 0, allele_frequencies)
+    r = [radius] * N
+    info = ['info'] * N
+
+    colors = [v['color'] for v in variant_ls]
+
+    hover_colors = [lighten_hex_color(c, 40) for c in colors]
+
+    source = ColumnDataSource(dict(x=x, r=r, y0=y0s, y1_circle=y1_ci_li_ct, y1_segment=y1_sg_li_ct,
+                                   y1_ci_li_ct=y1_ci_li_ct, y1_sg_li_ct=y1_sg_li_ct,
+                                   y1_ci_lg_ct=y1_ci_lg_ct, y1_sg_lg_ct=y1_sg_lg_ct,
+                                   y1_ci_li_fr=y1_ci_li_fr, y1_sg_li_fr=y1_sg_li_fr,
+                                   y1_ci_lg_fr=y1_ci_lg_fr, y1_sg_lg_fr=y1_sg_lg_fr,
+                                   allele_counts=allele_counts,
+                                   allele_numbers=allele_numbers,
+                                   allele_frequencies=allele_frequencies,
+                                   pos=[v['pos'] for v in variant_ls],
+                                   ref=[v['ref'] for v in variant_ls],
+                                   alt=[v['alt'] for v in variant_ls],
+                                   ann=[v['annotation'] for v in variant_ls],
+                                   sev=[v['severity'] for v in variant_ls],
+                                   colors=colors, hover_colors=hover_colors, line_alpha=[1 for v in variant_ls]))
+
+    segment_glyph = plot.segment(source=source, x0='x', y0='y0', x1='x', y1='y1_segment', line_color='colors',
+                                 line_width=line_width, line_alpha='line_alpha')
+    segment_glyph.hover_glyph = Segment(x0='x', y0='y0', x1='x', y1='y1_segment', line_color='hover_colors',
+                                        line_width=line_width, line_alpha='line_alpha')
+    segment_glyph.nonselection_glyph = None
+    circle_glyph = plot.circle('x', 'y1_circle', source=source, radius='r', radius_units='screen', fill_color='white',
+                               fill_alpha=0, line_color='colors', line_width=line_width + 0.5, line_alpha='line_alpha')
+    circle_glyph.hover_glyph = Circle(x='x', y='y1_circle', radius='r', radius_units='screen', fill_color='white',
+                                      fill_alpha=0, line_color='hover_colors', line_width=line_width + 0.5,
+                                      line_alpha='line_alpha')
+    circle_glyph.nonselection_glyph = None
+    return segment_glyph, circle_glyph, allele_counts, allele_frequencies
+
+
+def add_track_glyph(plot, tracks, height, y_pos):
+    tracks = [di for di in tracks if di['compact_start']>=0]
+    tracks = sorted(tracks, key=lambda di: di['end']-di['start'], reverse=True) #make sure smaller tracks are in front of larger tracks
+    tracks_compact = [(di['compact_start'], di['compact_end']) for di in tracks]
+    tracks_original = [(di['start'], di['end']) for di in tracks]
+    track_names = [di['ID'] for di in tracks]
+    colors = [di['color'] for di in tracks]
+
+    x = [center_feature(f) for f in tracks_compact]
+    y = [y_pos for f in tracks_compact]
+    w = [end - start for (start, end) in tracks_compact]
+    h = [height for f in tracks_compact]
+    hover_colors = [lighten_hex_color(color, 40) for color in colors]
+
+    # metadata
+    adj_start = [start for (start, end) in tracks_compact]
+    adj_end = [end for (start, end) in tracks_compact]
+    true_start = [start for (start, end) in tracks_original]
+    true_end = [end for (start, end) in tracks_original]
+    true_len = [end - start + 1 for (start, end) in tracks_original]  # +1 for 1 indexed coords
+
+    source = ColumnDataSource(dict(x=x, y=y, w=w, h=h, colors=colors, hover_colors=hover_colors,
+                                   track_names=track_names,
+                                   adj_start=adj_start, adj_end=adj_end,
+                                   true_len=true_len, true_start=true_start, true_end=true_end))
+
+    track_glyph = plot.rect(source=source, x='x', y='y', width='w', height='h', height_units='screen',
+                             fill_color='colors', line_color='colors')
+    hover_glyph = Rect(x='x', y='y', width='hover_w', height='h', height_units='screen', fill_color='hover_colors',
+                       line_color='hover_colors')
+    track_glyph.hover_glyph = hover_glyph
+    track_glyph.nonselection_glyph = None
+    return track_glyph
+
+
+def add_multi_line_glyph(plot_params, plot, xs_ls, ys_ls_unsmoothed, max_y=-1, k=1, y0=0, p=False, fill_area=False,
+                         y_axis_name=None, line_color='black', line_width=2, line_alpha=1):
+    def smooth_ls(ls, k=1):
+        ls_copy = ls
+        for i in range(0, len(ls_copy), k):
+            window_avg = np.mean(ls_copy[i:i + k])
+            for j in range(i, i + k):
+                if j < len(ls_copy): ls_copy[j] = float(window_avg)
+        return ls_copy
+
+    if max_y < 0: max_y = max([y for ys in ys_ls_unsmoothed for y in ys])
+
+    ys_ls_unsmoothed = [[y * (plot_params['plot_height'] - y0) / max_y + y0 for y in ys] for ys in ys_ls_unsmoothed]
+
+    ys_ls_smoothed = [smooth_ls(ys, k=k) for ys in ys_ls_unsmoothed]
+
+    line_alpha = [line_alpha for xs in xs_ls]
+
+    if fill_area:
+        xs_ls = [[xs[0]] + xs + [xs[-1]] for xs in xs_ls]
+        ys_ls_smoothed = [[y0] + ys + [y0] for ys in ys_ls_smoothed]
+        ys_ls_unsmoothed = [[y0] + ys + [y0] for ys in ys_ls_unsmoothed]
+        source = ColumnDataSource(dict(x=xs_ls, y=ys_ls_smoothed, y_unsmoothed=ys_ls_unsmoothed, line_alpha=line_alpha))
+        multi_line_glyph = plot.patches(source=source, xs='x', ys='y', fill_color=line_color, fill_alpha='line_alpha',
+                                        line_alpha=0)
+    else:
+        source = ColumnDataSource(dict(x=xs_ls, y=ys_ls_smoothed, y_unsmoothed=ys_ls_unsmoothed, line_alpha=line_alpha))
+        multi_line_glyph = plot.multi_line(source=source, xs='x', ys='y', line_color=line_color, line_width=line_width,
+                                           line_alpha='line_alpha')
+
+    multi_line_glyph.nonselection_glyph = None
+    return multi_line_glyph
+
+
diff --git a/report/map_coords.py b/report/map_coords.py
new file mode 100755
index 0000000..0a6b76c
--- /dev/null
+++ b/report/map_coords.py
@@ -0,0 +1,26 @@
+from project_coords import map_box,map_point
+
+#x coords must be ints
+def map_line(line_coords,exons,chr_num=-1):
+    xs_ls = []
+    ys_ls = []
+    
+    if 'start' in line_coords[0].keys():
+        map_box(line_coords, exons)
+        for co in line_coords:
+            if co['compact_start'] < 0: continue
+            xs = list(range(co['compact_start'],co['compact_end']+1))
+            ys = []
+            for x in xs:
+                ys.append(co['y'])    
+            xs_ls.append(xs)
+            ys_ls.append(ys)
+    else:   
+        map_point(line_coords, exons)
+
+        for exon in exons:
+            exon_pts = [co for co in line_coords if exon['compact_start'] <= co['compact_pos'] <= exon['compact_end']]
+            xs_ls.append([co['compact_pos'] for co in exon_pts])
+            ys_ls.append([co['y'] for co in exon_pts])        
+
+    return xs_ls,ys_ls
\ No newline at end of file
diff --git a/report/named_colors.yaml b/report/named_colors.yaml
new file mode 100755
index 0000000..a066a2e
--- /dev/null
+++ b/report/named_colors.yaml
@@ -0,0 +1,91 @@
+#Color names from coolors.co
+
+#REDS
+red salsa: '#f94144'
+orange red: '#f3722c'
+maroon: '#a53860'
+irresistible: '#b4436c'
+big dip oruby: '#982649'
+rust: '#bf3100'
+rose madder: '#db2b39'
+carmine: '#d62246'
+vermillion: '#c73e1d'
+burgundy: '#7d1128'
+
+
+#ORANGES
+yellow orange: '#f8961e'
+mango tango: '#ff8c42'
+sandy brown: #ee964b'
+orange soda: '#f95738'
+dark orange: '#ff9000'
+cadmium orange: '#dd8740'
+alloy orange: '#bf6822'
+russet : '#7a4419'
+safety orange: '#f26419'
+mahogany: '#c14b0b'
+
+#YELLOWS
+maize crayola: 'f9c74f'
+maxiumum yellow red: '#f7b538'
+marigold: '#ec9f05'
+orange yellow: '#f5bb00'
+honey yellow: '#f6ae2d'
+corn: '#fff05a'
+saffron: '#e9ba20'
+satin sheen gold: '#cba135'
+metallic sunburst: '#a2802a'
+lemon curry: '#ad9A0b'
+
+#GREENS
+pistachio: '#90be6d'
+shiny shamrock: '#49a078'
+bud green: '#5fad56'
+illuminating emerald: '#4d9078'
+warm black: '#104547'
+dark green: '#90C290'
+moss green: '#809848'
+yellow green: '#8Fc93a'
+avocado: '#5c8001'
+polished pine: '#6ba292'
+apple green: '#80b918'
+
+#BLUES
+zomp: '#43aa8b'
+queen blue: '#577590'
+medium slate blue: '#7161ef'
+purple navy: '#404e7c'
+ocean blue: '#613dc1'
+indigo dye: '#0d3b66'
+wild blue yonder: '#a1b5d8'
+oxford blue: '#031d44'
+dark sky blue: '#86bbd8'
+charcoal: '#2f4858'
+
+#PURPLES
+bright lilac: '#bf99f2'
+rhythm: '#7e7f9a'
+orchid crayola: '#e899dc'
+violet web: '#e086d3'
+maximum blue purple: '#a09be7'
+plum web: '#eda2f2'
+dark orchid: '#af2bbf'
+dark purple: '#4b1d3f'
+old mauve: '#5d2e46'
+razzmic berry: '#9b5094'
+
+#PINKS
+dogwood rose: '#d90368'
+quinacridone magenta: '#993955'
+super pink: '#dc6bad'
+ultra red: '#ef798a'
+pastel pink: '#f7a9a8'
+cinnamon satin: '#ce6d8b'
+vivid burgundy: '#990033'
+claret: '#5f021f'
+light coral: '#f28482'
+fuzzy wuzzy: '#cd5d67'
+
+#GRAYS
+gray 11: '#bdbdbd'
+davys gray: '#525252'
\ No newline at end of file
diff --git a/report/observed_mut_counts.txt b/report/observed_mut_counts.txt
new file mode 100755
index 0000000..c0845a1
--- /dev/null
+++ b/report/observed_mut_counts.txt
@@ -0,0 +1,2899 @@
+20	63400208	3
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diff --git a/report/palettes.yaml b/report/palettes.yaml
new file mode 100755
index 0000000..11ae093
--- /dev/null
+++ b/report/palettes.yaml
@@ -0,0 +1,8 @@
+#colors can be RGB (#xxxxxx or xxxxxx), or named colors from named_colors.yaml
+reds: [
+  'red salsa', 'orange red', 'maroon', 'irresistible', 'big dip oruby', 'rust', 'rose madder', 'carmine', 'vermillion', 'burgundy',
+]
+
+blues: [
+  'zomp', 'queen blue', 'medium slate blue', 'purple navy', 'ocean blue', 'indigo dye', 'wild blue yonder', 'oxford blue', 'dark sky blue', 'charcoal',
+]
\ No newline at end of file
diff --git a/report/plot.html b/report/plot.html
new file mode 100644
index 0000000..253afb9
--- /dev/null
+++ b/report/plot.html
@@ -0,0 +1,86 @@
+
+
+
+
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+        <script type="text/javascript">
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+</html>
\ No newline at end of file
diff --git a/report/project_coords.py b/report/project_coords.py
new file mode 100755
index 0000000..32a23ee
--- /dev/null
+++ b/report/project_coords.py
@@ -0,0 +1,484 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Aug 24 12:40:23 2021
+
+@author: slulla
+"""
+
+def adjust_coordinates(exons, intron_size=10):
+    
+    '''
+    UNIT TEST 1 - intron at 0
+    >>> ec1 = [{'start': 100, 'end': 200}, {'start': 250, 'end': 400}, {'start': 700, 'end': 900}]
+    >>> adjust_coordinates(ec1)
+    >>> for exon in ec1: print(exon)
+    {'start': 100, 'end': 200, 'compact_start': 10, 'compact_end': 110}
+    {'start': 250, 'end': 400, 'compact_start': 120, 'compact_end': 270}
+    {'start': 700, 'end': 900, 'compact_start': 280, 'compact_end': 480}
+    
+    UNIT TEST 2 - exon at 0
+    >>> ec2 = [{'start': 0, 'end': 200}, {'start': 250, 'end': 400}, {'start': 700, 'end': 900}]
+    >>> adjust_coordinates(ec2)
+    >>> for exon in ec2: print(exon)
+    {'start': 0, 'end': 200, 'compact_start': 0, 'compact_end': 200}
+    {'start': 250, 'end': 400, 'compact_start': 210, 'compact_end': 360}
+    {'start': 700, 'end': 900, 'compact_start': 370, 'compact_end': 570}
+    
+    UNIT TEST 3 - intron at 0, intron_size=20
+    >>> ec3 = [{'start': 100, 'end': 200}, {'start': 250, 'end': 400}, {'start': 700, 'end': 900}]
+    >>> adjust_coordinates(ec3, intron_size=20)
+    >>> for exon in ec3: print(exon)
+    {'start': 100, 'end': 200, 'compact_start': 20, 'compact_end': 120}
+    {'start': 250, 'end': 400, 'compact_start': 140, 'compact_end': 290}
+    {'start': 700, 'end': 900, 'compact_start': 310, 'compact_end': 510}
+    
+    UNIT TEST 4 - exon at 0, intron_size=20
+    >>> ec4 = [{'start': 0, 'end': 200}, {'start': 250, 'end': 400}, {'start': 700, 'end': 900}]
+    >>> adjust_coordinates(ec4, intron_size=20)
+    >>> for exon in ec4: print(exon)
+    {'start': 0, 'end': 200, 'compact_start': 0, 'compact_end': 200}
+    {'start': 250, 'end': 400, 'compact_start': 220, 'compact_end': 370}
+    {'start': 700, 'end': 900, 'compact_start': 390, 'compact_end': 590}
+    
+    UNIT TEST 5 - 1 intron length < intron_size
+    >>> ec5 = [{'start': 0, 'end': 200}, {'start': 250, 'end': 400}, {'start': 410, 'end': 610}]
+    >>> adjust_coordinates(ec5, intron_size=20)
+    >>> for exon in ec5: print(exon)
+    {'start': 0, 'end': 200, 'compact_start': 0, 'compact_end': 200}
+    {'start': 250, 'end': 400, 'compact_start': 220, 'compact_end': 370}
+    {'start': 410, 'end': 610, 'compact_start': 380, 'compact_end': 580}
+    
+     UNIT TEST 6 - backwards coordinates
+     >>> ec6 = [{'start': 900, 'end': 700}, {'start': 400, 'end': 250}, {'start': 200, 'end': 100}]
+     >>> adjust_coordinates(ec6)
+     >>> for exon in ec6: print(exon)
+     {'start': 700, 'end': 900, 'compact_start': 280, 'compact_end': 480}
+     {'start': 250, 'end': 400, 'compact_start': 120, 'compact_end': 270}
+     {'start': 100, 'end': 200, 'compact_start': 10, 'compact_end': 110}
+     
+     UNIT TEST 7 - empty input
+     >>> ec7 = []
+     >>> adjust_coordinates(ec7)
+     >>> for exon in ec7: print(exon)
+
+     UNIT TEST 8 - overlapping exon coordinates
+     >>> ec8 = [{'start': 0, 'end': 200}, {'start': 100, 'end': 300}, {'start': 400, 'end': 500}]
+     >>> adjust_coordinates(ec8)
+     Traceback (most recent call last):
+         ...
+     ValueError: Exon coordinates overlap
+    '''
+
+    def flip_exon_coords(exons):
+        for exon in exons:
+            tmp = exon['start']
+            exon['start'] = exon['end']
+            exon['end'] = tmp
+    
+   
+    if len(exons) == 0: return
+    
+    #if exon coordinates are backwards, flip them
+    if exons[0]['start'] > exons[0]['end']: 
+        flip_exon_coords(exons)
+    
+    exons = sorted(exons, key=lambda exon:exon['start'])
+    
+    end_last_compact = 0 #end of last exon in compacted coords
+    end_last_original = 0 #end of last exon in original coords
+    
+    for idx,exon in enumerate(exons):
+        
+        if end_last_original > exon['start']: raise ValueError('Exon coordinates overlap')
+        
+        if exon['start'] == 0:
+            exon['compact_start'] = exon['start']
+            exon['compact_end'] = exon['end']
+            
+            end_last_compact = exon['end']
+            end_last_original = exon['end']
+            continue
+        
+        intron_len = exon['start'] - end_last_original #length of intron between this exon and previous
+        new_start = end_last_compact+intron_size if intron_len > intron_size else end_last_compact+intron_len
+        new_end = new_start + exon['end'] - exon['start'] ###1 based or 0 based coordinate system?###
+        exon['compact_start'] = new_start
+        exon['compact_end'] = new_end
+            
+        end_last_compact = new_end
+        end_last_original = exon['end']
+
+def flatten_exons(exons):
+    
+    '''
+    UNIT TEST 1 - no overlaps
+    >>> e1 = [{'start': 150, 'end': 200}, {'start': 0, 'end': 100}, {'start': 300, 'end': 450}, {'start': 500, 'end': 600}]
+    >>> flatten_exons(e1)
+    [{'start': 0, 'end': 100}, {'start': 150, 'end': 200}, {'start': 300, 'end': 450}, {'start': 500, 'end': 600}]
+    
+    UNIT TEST 2 - all overlaps
+    >>> e2 = [{'start': 50, 'end': 100}, {'start': 75, 'end': 150}, {'start': 0, 'end': 80}, {'start': 120, 'end': 130}]
+    >>> flatten_exons(e2)
+    [{'start': 0, 'end': 150}]
+
+    UNIT TEST 3 - start with overlaps
+    >>> e3 = [{'start': 10, 'end': 50}, {'start': 40, 'end': 70}, {'start': 60, 'end': 80}, {'start': 100, 'end': 150}, {'start': 160, 'end': 200}, {'start': 300, 'end': 350}]
+    >>> flatten_exons(e3)
+    [{'start': 10, 'end': 80}, {'start': 100, 'end': 150}, {'start': 160, 'end': 200}, {'start': 300, 'end': 350}]
+    
+    UNIT TEST 4 - end with overlaps
+    >>> e4 = [{'start': 50, 'end': 100}, {'start': 150, 'end': 200}, {'start': 250, 'end': 350}, {'start': 375, 'end': 390}, {'start': 325, 'end': 400}, {'start': 270, 'end': 320}, {'start': 400, 'end': 450}, {'start': 380, 'end': 450}, {'start': 450, 'end': 500}]
+    >>> flatten_exons(e4)
+    [{'start': 50, 'end': 100}, {'start': 150, 'end': 200}, {'start': 250, 'end': 500}]
+    
+    UNIT TEST 5 - overlaps only in middle
+    >>> e5 = [{'start': 200, 'end': 250}, {'start': 275, 'end': 300}, {'start': 350, 'end': 400}, {'start': 310, 'end': 400}, {'start': 360, 'end': 380}, {'start': 400, 'end': 410}, {'start': 450, 'end': 500}]
+    >>> flatten_exons(e5)
+    [{'start': 200, 'end': 250}, {'start': 275, 'end': 300}, {'start': 310, 'end': 410}, {'start': 450, 'end': 500}]
+
+    '''
+        
+    exon_coords = [(exon['start'],exon['end']) for exon in exons]
+    
+    def largest_range(ls):
+        min_start = min([start for (start,end) in ls])
+        max_end = max([end for (start,end) in ls])
+        return (min_start, max_end)
+
+    exon_coords = sorted(exon_coords, key=lambda x:x[0]) #sort by starting coord
+    
+    exons_flat = [] #list to return
+    overlaps = [exon_coords[0]] #list of overlapping exons
+    max_end = exon_coords[0][1] #end of overlapping region
+
+    for i in range(1, len(exon_coords)): 
+        if exon_coords[i][0] <= max_end: #if start of this exon is before end of overlapping region:
+            overlaps.append(exon_coords[i]) #add this exon to overlapping region
+            if exon_coords[i][1] > max_end: max_end = exon_coords[i][1]
+        else:
+            if len(overlaps) == 1: exons_flat.append(overlaps[0])
+            if len(overlaps) > 1: exons_flat.append(largest_range(overlaps))
+            overlaps = [exon_coords[i]]
+            max_end = exon_coords[i][1]
+
+    exons_flat.append(largest_range(overlaps)) #have to do this one more time at the end
+    exons_flat = sorted(exons_flat, key=lambda x:x[0]) #sort by starting coord
+    
+    exons = []
+    for idx,e in enumerate(exons_flat):
+        exons.append(dict(start=e[0],end=e[1]))    
+    return exons
+
+
+
+def map_box(box_coords, exons):
+    '''
+    UNIT TEST 1 - one box inside each exon
+    >>> ec1 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> bc1 = [{'start': 150, 'end': 175}, {'start': 300, 'end': 375}, {'start': 800, 'end': 825}]
+    >>> adjust_coordinates(ec1)
+    >>> map_box(bc1, ec1)
+    >>> for coord in bc1: print(coord)
+    {'start': 150, 'end': 175, 'compact_start': 60, 'compact_end': 85}
+    {'start': 300, 'end': 375, 'compact_start': 170, 'compact_end': 245}
+    {'start': 800, 'end': 825, 'compact_start': 380, 'compact_end': 405}
+    
+    UNIT TEST 2 - >= 1 box inside each exon 
+    >>> ec2 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> bc2 = [{'start': 150, 'end': 160}, {'start': 170, 'end': 190}, {'start': 270, 'end': 290}, {'start': 300, 'end': 350}, {'start': 360, 'end': 375}, {'start': 800, 'end': 825}, {'start': 830, 'end': 880}]
+    >>> adjust_coordinates(ec2)
+    >>> map_box(bc2, ec2)
+    >>> for coord in bc2: print(coord)
+    {'start': 150, 'end': 160, 'compact_start': 60, 'compact_end': 70}
+    {'start': 170, 'end': 190, 'compact_start': 80, 'compact_end': 100}
+    {'start': 270, 'end': 290, 'compact_start': 140, 'compact_end': 160}
+    {'start': 300, 'end': 350, 'compact_start': 170, 'compact_end': 220}
+    {'start': 360, 'end': 375, 'compact_start': 230, 'compact_end': 245}
+    {'start': 800, 'end': 825, 'compact_start': 380, 'compact_end': 405}
+    {'start': 830, 'end': 880, 'compact_start': 410, 'compact_end': 460}
+        
+    UNIT TEST 3 - 2 exons without a box
+    >>> ec3 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> bc3 = [{'start': 260, 'end': 300}, {'start': 330, 'end': 370}]
+    >>> adjust_coordinates(ec3)
+    >>> map_box(bc3, ec3)
+    >>> for coord in bc3: print(coord)
+    {'start': 260, 'end': 300, 'compact_start': 130, 'compact_end': 170}
+    {'start': 330, 'end': 370, 'compact_start': 200, 'compact_end': 240}
+    
+    
+    UNIT TEST 4 - boxes partially in exons
+    >>> ec4 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> bc4 = [{'start': 180, 'end': 210}, {'start': 230, 'end': 300}, {'start': 320, 'end': 420}, {'start': 660, 'end': 800}, {'start': 820, 'end': 850}]
+    >>> adjust_coordinates(ec4)
+    >>> map_box(bc4, ec4)
+    >>> for coord in bc4: print(coord)
+    {'start': 180, 'end': 210, 'compact_start': 90, 'compact_end': 110}
+    {'start': 230, 'end': 300, 'compact_start': 120, 'compact_end': 170}
+    {'start': 320, 'end': 420, 'compact_start': 190, 'compact_end': 270}
+    {'start': 660, 'end': 800, 'compact_start': 280, 'compact_end': 380}
+    {'start': 820, 'end': 850, 'compact_start': 400, 'compact_end': 430}
+    
+    UNIT TEST 5 - boxes on exon boundaries
+    >>> ec5 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> bc5 = [{'start': 100, 'end': 200}, {'start': 250, 'end': 300}, {'start': 700, 'end': 725}, {'start': 750, 'end': 900}]
+    >>> adjust_coordinates(ec5)
+    >>> map_box(bc5, ec5)
+    >>> for coord in bc5: print(coord)
+    {'start': 100, 'end': 200, 'compact_start': 10, 'compact_end': 110}
+    {'start': 250, 'end': 300, 'compact_start': 120, 'compact_end': 170}
+    {'start': 700, 'end': 725, 'compact_start': 280, 'compact_end': 305}
+    {'start': 750, 'end': 900, 'compact_start': 330, 'compact_end': 480}
+    
+    UNIT TEST 6 - boxes in introns
+    >>> ec6 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> bc6 = [{'start': 0, 'end': 90}, {'start': 210, 'end': 220}, {'start': 230, 'end': 240}, {'start': 1000, 'end': 1100}]
+    >>> adjust_coordinates(ec6)
+    >>> map_box(bc6, ec6)
+    >>> for coord in bc6: print(coord)
+    {'start': 0, 'end': 90, 'compact_start': -1, 'compact_end': -1}
+    {'start': 210, 'end': 220, 'compact_start': -1, 'compact_end': -1}
+    {'start': 230, 'end': 240, 'compact_start': -1, 'compact_end': -1}
+    {'start': 1000, 'end': 1100, 'compact_start': -1, 'compact_end': -1}
+    
+    UNIT TEST 7 - boxes in introns, starting at last base of previous exon and/or ending at last base of next exon
+    >>> ec7 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> bc7 = [{'start': 50, 'end': 100}, {'start': 200, 'end': 210}, {'start': 220, 'end': 250}, {'start': 400, 'end': 500}, {'start': 400, 'end': 700}, {'start': 900, 'end': 950}]
+    >>> adjust_coordinates(ec7)
+    >>> map_box(bc7, ec7)
+    >>> for coord in bc7: print(coord)
+    {'start': 50, 'end': 100, 'compact_start': -1, 'compact_end': -1}
+    {'start': 200, 'end': 210, 'compact_start': -1, 'compact_end': -1}
+    {'start': 220, 'end': 250, 'compact_start': -1, 'compact_end': -1}
+    {'start': 400, 'end': 500, 'compact_start': -1, 'compact_end': -1}
+    {'start': 400, 'end': 700, 'compact_start': -1, 'compact_end': -1}
+    {'start': 900, 'end': 950, 'compact_start': -1, 'compact_end': -1}
+    
+    UNIT TEST 8 - start and end coordinates reversed
+    >>> ec8 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> bc8 = [{'start': 210, 'end': 180}, {'start': 420, 'end': 320}, {'start': 800, 'end': 660}, {'start': 850, 'end': 820}]
+    >>> adjust_coordinates(ec8)
+    >>> map_box(bc8, ec8)
+    >>> for coord in bc8: print(coord)
+    {'start': 180, 'end': 210, 'compact_start': 90, 'compact_end': 110}
+    {'start': 320, 'end': 420, 'compact_start': 190, 'compact_end': 270}
+    {'start': 660, 'end': 800, 'compact_start': 280, 'compact_end': 380}
+    {'start': 820, 'end': 850, 'compact_start': 400, 'compact_end': 430}
+    
+    UNIT TEST 9 - overlapping boxes
+    >>> ec9 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> bc9 = [{'start': 125, 'end': 175}, {'start': 140, 'end': 190}, {'start': 200, 'end': 300}, {'start': 270, 'end': 370}, {'start': 700, 'end': 850}, {'start': 820, 'end': 870}, {'start': 800, 'end': 900}]
+    >>> adjust_coordinates(ec9)
+    >>> map_box(bc9, ec9)
+    >>> for coord in bc9: print(coord)
+    {'start': 125, 'end': 175, 'compact_start': 35, 'compact_end': 85}
+    {'start': 140, 'end': 190, 'compact_start': 50, 'compact_end': 100}
+    {'start': 200, 'end': 300, 'compact_start': 120, 'compact_end': 170}
+    {'start': 270, 'end': 370, 'compact_start': 140, 'compact_end': 240}
+    {'start': 700, 'end': 850, 'compact_start': 280, 'compact_end': 430}
+    {'start': 820, 'end': 870, 'compact_start': 400, 'compact_end': 450}
+    {'start': 800, 'end': 900, 'compact_start': 380, 'compact_end': 480}
+    
+    UNIT TEST 10 - boxes out of order
+    >>> ec10 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> bc10 = [{'start': 230, 'end': 300}, {'start': 180, 'end': 210}, {'start': 820, 'end': 850}, {'start': 320, 'end': 420}, {'start': 660, 'end': 800}]
+    >>> adjust_coordinates(ec10)
+    >>> map_box(bc10, ec10)
+    >>> for coord in bc10: print(coord)
+    {'start': 230, 'end': 300, 'compact_start': 120, 'compact_end': 170}
+    {'start': 180, 'end': 210, 'compact_start': 90, 'compact_end': 110}
+    {'start': 820, 'end': 850, 'compact_start': 400, 'compact_end': 430}
+    {'start': 320, 'end': 420, 'compact_start': 190, 'compact_end': 270}
+    {'start': 660, 'end': 800, 'compact_start': 280, 'compact_end': 380}
+    
+    UNIT TEST 11 - empty box list
+    >>> ec11 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> bc11 = []
+    >>> adjust_coordinates(ec11)
+    >>> map_box(bc11, ec11)
+    >>> for coord in bc11: print(coord)
+    
+    UNIT TEST 12 - empty exon list
+    >>> ec12 = []
+    >>> bc12 = [{'start': 150, 'end': 175}, {'start': 300, 'end': 375}, {'start': 800, 'end': 825}]
+    >>> adjust_coordinates(ec12)
+    >>> map_box(bc12, ec12)
+    >>> for coord in bc12: print(coord)
+    {'start': 150, 'end': 175, 'compact_start': -1, 'compact_end': -1}
+    {'start': 300, 'end': 375, 'compact_start': -1, 'compact_end': -1}
+    {'start': 800, 'end': 825, 'compact_start': -1, 'compact_end': -1}
+    
+    UNIT TEST 13 - >= 1 box inside each exon with intron_size=20
+    >>> ec13 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> bc13 = [{'start': 150, 'end': 160}, {'start': 170, 'end': 190}, {'start': 270, 'end': 290}, {'start': 300, 'end': 350}, {'start': 360, 'end': 375}, {'start': 800, 'end': 825}, {'start': 830, 'end': 880}]
+    >>> adjust_coordinates(ec13, intron_size=20)
+    >>> map_box(bc13, ec13)
+    >>> for coord in bc13: print(coord)
+    {'start': 150, 'end': 160, 'compact_start': 70, 'compact_end': 80}
+    {'start': 170, 'end': 190, 'compact_start': 90, 'compact_end': 110}
+    {'start': 270, 'end': 290, 'compact_start': 160, 'compact_end': 180}
+    {'start': 300, 'end': 350, 'compact_start': 190, 'compact_end': 240}
+    {'start': 360, 'end': 375, 'compact_start': 250, 'compact_end': 265}
+    {'start': 800, 'end': 825, 'compact_start': 410, 'compact_end': 435}
+    {'start': 830, 'end': 880, 'compact_start': 440, 'compact_end': 490}
+    
+    
+    '''
+    
+    for b in box_coords:
+        if b['start'] > b['end']:
+            tmp = b['start']
+            b['start'] = b['end']
+            b['end'] = tmp
+        b['compact_start'] = -1
+        b['compact_end'] = -1
+        for exon in exons:
+            if exon['end'] <= b['start'] or exon['start'] >= b['end']: continue
+            b_start_compact = exon['compact_start'] if b['start'] < exon['start'] else exon['compact_start'] + b['start'] - exon['start']
+            b_end_compact = exon['compact_end'] if b['end'] > exon['end'] else exon['compact_end'] - (exon['end'] - b['end'])
+            b['compact_start'] = b_start_compact
+            b['compact_end'] = b_end_compact
+            break
+
+def map_point(point_coords, exons):
+    
+    '''
+    UNIT TEST 1 - 1 point inside each exon
+    >>> ec1 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> pc1 = [{'pos': 150}, {'pos': 300}, {'pos': 800},]
+    >>> adjust_coordinates(ec1)
+    >>> map_point(pc1, ec1)
+    >>> for coord in pc1: print(coord)
+    {'pos': 150, 'compact_pos': 60}
+    {'pos': 300, 'compact_pos': 170}
+    {'pos': 800, 'compact_pos': 380}
+    
+    UNIT TEST 2 - >=1 point inside each exon
+    >>> ec2 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> pc2 = [{'pos': 150}, {'pos': 175}, {'pos': 300}, {'pos': 750}, {'pos': 800}, {'pos': 850}]
+    >>> adjust_coordinates(ec2)
+    >>> map_point(pc2, ec2)
+    >>> for coord in pc2: print(coord)
+    {'pos': 150, 'compact_pos': 60}
+    {'pos': 175, 'compact_pos': 85}
+    {'pos': 300, 'compact_pos': 170}
+    {'pos': 750, 'compact_pos': 330}
+    {'pos': 800, 'compact_pos': 380}
+    {'pos': 850, 'compact_pos': 430}
+    
+    UNIT TEST 3 - 2 exons without a point
+    >>> ec2 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> pc2 = [{'pos': 300}, {'pos': 350}]
+    >>> adjust_coordinates(ec2)
+    >>> map_point(pc2, ec2)
+    >>> for coord in pc2: print(coord)
+    {'pos': 300, 'compact_pos': 170}
+    {'pos': 350, 'compact_pos': 220}
+    
+    UNIT TEST 4 - points on exon boundaries
+    >>> ec4 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> pc4 = [{'pos': 100}, {'pos': 400}, {'pos': 900},]
+    >>> adjust_coordinates(ec4)
+    >>> map_point(pc4, ec4)
+    >>> for coord in pc4: print(coord)
+    {'pos': 100, 'compact_pos': 10}
+    {'pos': 400, 'compact_pos': 270}
+    {'pos': 900, 'compact_pos': 480}
+    
+    UNIT TEST 5 - points in introns
+    >>> ec5 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> pc5 = [{'pos': 50}, {'pos': 210}, {'pos': 240}, {'pos': 500}, {'pos': 950},]
+    >>> adjust_coordinates(ec5)
+    >>> map_point(pc5, ec5)
+    >>> for coord in pc5: print(coord)
+    {'pos': 50, 'compact_pos': -1}
+    {'pos': 210, 'compact_pos': -1}
+    {'pos': 240, 'compact_pos': -1}
+    {'pos': 500, 'compact_pos': -1}
+    {'pos': 950, 'compact_pos': -1}
+   
+    UNIT TEST 6 - overlapping points
+    >>> ec6 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> pc6 = [{'pos': 150}, {'pos': 150}, {'pos': 240}, {'pos': 240}, {'pos': 750}, {'pos': 750}]
+    >>> adjust_coordinates(ec6)
+    >>> map_point(pc6, ec6)
+    >>> for coord in pc6: print(coord)
+    {'pos': 150, 'compact_pos': 60}
+    {'pos': 150, 'compact_pos': 60}
+    {'pos': 240, 'compact_pos': -1}
+    {'pos': 240, 'compact_pos': -1}
+    {'pos': 750, 'compact_pos': 330}
+    {'pos': 750, 'compact_pos': 330}
+   
+    UNIT TEST 7 - points out of order
+    >>> ec7 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> pc7 = [{'pos': 800}, {'pos': 175}, {'pos': 300}, {'pos': 150}, {'pos': 850}, {'pos': 750}]
+    >>> adjust_coordinates(ec7)
+    >>> map_point(pc7, ec7)
+    >>> for coord in pc7: print(coord)
+    {'pos': 800, 'compact_pos': 380}
+    {'pos': 175, 'compact_pos': 85}
+    {'pos': 300, 'compact_pos': 170}
+    {'pos': 150, 'compact_pos': 60}
+    {'pos': 850, 'compact_pos': 430}
+    {'pos': 750, 'compact_pos': 330}
+    
+    UNIT TEST 8 - empty point list
+    >>> ec8 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> pc8 = []
+    >>> adjust_coordinates(ec8)
+    >>> map_point(pc8, ec8)
+    >>> for coord in pc8: print(coord)
+    
+    UNIT TEST 9 - empty exon list
+    >>> ec9 = []
+    >>> pc9 = [{'pos': 150}, {'pos': 300}, {'pos': 800},]
+    >>> adjust_coordinates(ec9)
+    >>> map_point(pc9, ec9)
+    >>> for coord in pc9: print(coord)
+    {'pos': 150, 'compact_pos': -1}
+    {'pos': 300, 'compact_pos': -1}
+    {'pos': 800, 'compact_pos': -1}
+    
+    UNIT TEST 10 - >=1 point inside each exon with intron_size=20
+    >>> ec10 = [{'start': 100, 'end': 200},{'start': 250, 'end': 400},{'start': 700, 'end': 900}]
+    >>> pc10 = [{'pos': 150}, {'pos': 175}, {'pos': 300}, {'pos': 750}, {'pos': 800}, {'pos': 850}]
+    >>> adjust_coordinates(ec10, intron_size=20)
+    >>> map_point(pc10, ec10)
+    >>> for coord in pc10: print(coord)
+    {'pos': 150, 'compact_pos': 70}
+    {'pos': 175, 'compact_pos': 95}
+    {'pos': 300, 'compact_pos': 190}
+    {'pos': 750, 'compact_pos': 360}
+    {'pos': 800, 'compact_pos': 410}
+    {'pos': 850, 'compact_pos': 460}
+    
+    '''
+    
+    for coord in point_coords:
+        coord['compact_pos'] = -1
+        for exon in exons:
+            if coord['pos'] >= exon['start'] and coord['pos'] <= exon['end']:
+                coord['compact_pos'] = exon['compact_start'] + coord['pos'] - exon['start']
+                break
+
+
+def get_introns_from_exons(exons):
+    introns = []
+
+    flat_exons = [(exon['start'], exon['end']) for exon in exons]
+    flat_exons = [item for sublist in flat_exons for item in sublist][:-1]
+    if len(flat_exons) % 2 == 1: flat_exons = [0] + flat_exons
+
+    flat_exons_compact = [(exon['compact_start'], exon['compact_end']) for exon in exons]
+    flat_exons_compact = [item for sublist in flat_exons_compact for item in sublist][:-1]
+    if len(flat_exons_compact) % 2 == 1: flat_exons_compact = [0] + flat_exons_compact
+    for i in range(0, len(flat_exons) - 1, 2):
+        introns.append({'start': flat_exons[i] + 1, 'end': flat_exons[i + 1] - 1,
+                        'compact_start': flat_exons_compact[i] + 1, 'compact_end': flat_exons_compact[i + 1] - 1})
+    return introns
+
+
+if __name__ == "__main__":
+    import doctest
+    doctest.testmod()
\ No newline at end of file
diff --git a/report/test.py b/report/test.py
new file mode 100755
index 0000000..1a7b6d7
--- /dev/null
+++ b/report/test.py
@@ -0,0 +1,2 @@
+import sys
+print(sys.argv[1])
diff --git a/report/test1.html b/report/test1.html
new file mode 100644
index 0000000..22f23b0
--- /dev/null
+++ b/report/test1.html
@@ -0,0 +1,86 @@
+
+
+
+
+<!DOCTYPE html>
+<html lang="en">
+  
+  <head>
+    
+      <meta charset="utf-8">
+      <title>Bokeh Plot</title>
+      
+      
+        
+          
+        
+        
+          
+        <script type="text/javascript" src="https://cdn.bokeh.org/bokeh/release/bokeh-2.3.3.min.js" integrity="sha384-dM3QQsP+wXdHg42wTqW85BjZQdLNNIXqlPw/BgKoExPmTG7ZLML4EGqLMfqHT6ON" crossorigin="anonymous"></script>
+        <script type="text/javascript" src="https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.3.3.min.js" integrity="sha384-3QTqdz9LyAm2i0sG5XTePsHec3UHWwVsrOL68SYRoAXsafvfAyqtQ+h440+qIBhS" crossorigin="anonymous"></script>
+        <script type="text/javascript">
+            Bokeh.set_log_level("info");
+        </script>
+        
+      
+      
+    
+  </head>
+  
+  
+  <body>
+    
+      
+        
+          
+          
+            
+              <div class="bk-root" id="c548ba9d-37d4-4cb9-af17-e69b7a0bfe94" data-root-id="1444"></div>
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counts":[],"allele_frequency":[{"id":"1052"}],"count":[{"id":"1048"}]},"mlo_lg_ct":[{"114.25":"3.49","140.5":"3.79","166.75":"3.97","193":"4.09","88":"0.00"}],"mlo_lg_fr":[{"114.25":"1.70","140.5":"1.40","166.75":"1.22","193":"1.10","88":"0.00"}],"mlo_li_ct":[{"114.25":"3107.50","140.5":"6214.00","166.75":"9320.50","193":"12427.00","88":"1.00"}],"mlo_li_fr":[{"114.25":"0.02","140.5":"0.04","166.75":"0.06","193":"0.08","88":"0.00"}],"radio_group_scale":{"id":"1209"},"variant":[{"id":"1036"},{"id":"1042"}]},"code":"        \n        function setAxis(label, mlo){\n            for (let i = 0; i &lt; axes['count'].length; i++){\n                axes['count'][i].axis_label = label\n                axes['count'][i].major_label_overrides = mlo[i]\n            }   \n        }\n        \n        for (let i = 0; i &lt; variant.length; i++){\n            if (cb_obj.active == 0) {\n                if (radio_group_scale.active == 0){\n                    variant[i].data_source.data['y1_circle']=variant[i].data_source.data['y1_ci_li_ct']\n                    variant[i].data_source.data['y1_segment']=variant[i].data_source.data['y1_sg_li_ct']\n                    setAxis('Allele count', mlo_li_ct)\n                } else {\n                    variant[i].data_source.data['y1_circle']=variant[i].data_source.data['y1_ci_lg_ct']\n                    variant[i].data_source.data['y1_segment']=variant[i].data_source.data['y1_sg_lg_ct']\n                    setAxis('Log(Allele count)', mlo_lg_ct)\n                }\n            }\n            if (cb_obj.active == 1) {\n                if (radio_group_scale.active == 0){\n                    variant[i].data_source.data['y1_circle']=variant[i].data_source.data['y1_ci_li_fr']\n                    variant[i].data_source.data['y1_segment']=variant[i].data_source.data['y1_sg_li_fr']\n                    setAxis('Allele frequency', mlo_li_fr)\n                } else {\n                    variant[i].data_source.data['y1_circle']=variant[i].data_source.data['y1_ci_lg_fr']\n                    variant[i].data_source.data['y1_segment']=variant[i].data_source.data['y1_sg_lg_fr']\n                    setAxis('-Log(Allele frequency)', mlo_lg_fr)\n                }\n            }\n            variant[i].data_source.change.emit()        \n        }\n    "},"id":"1210","type":"CustomJS"},{"attributes":{},"id":"1014","type":"BasicTicker"},{"attributes":{},"id":"1437","type":"Selection"},{"attributes":{"height":15,"text":"Lollipop height scale:","width":200},"id":"1207","type":"Div"},{"attributes":{"active_drag":null,"active_multi":null,"tools":[{"id":"1021"},{"id":"1022"},{"id":"1023"},{"id":"1024"},{"id":"1045"},{"id":"1060"},{"id":"1073"},{"id":"1080"},{"id":"1089"},{"id":"1101"},{"id":"1113"}]},"id":"1026","type":"Toolbar"},{"attributes":{},"id":"1011","type":"LinearScale"},{"attributes":{},"id":"1438","type":"UnionRenderers"},{"attributes":{},"id":"1244","type":"Selection"},{"attributes":{"callback":null},"id":"1021","type":"TapTool"},{"attributes":{"background_fill_color":"white","below":[{"id":"1013"}],"center":[{"id":"1016"},{"id":"1020"},{"id":"1092"},{"id":"1104"},{"id":"1116"}],"extra_y_ranges":{"Allele count":{"id":"1047"},"Allele frequency":{"id":"1051"},"Number of mutations":{"id":"1140"},"Sequencing Coverage (30x)":{"id":"1124"}},"height":200,"left":[{"id":"1017"},{"id":"1048"},{"id":"1052"}],"min_border":0,"renderers":[{"id":"1036"},{"id":"1042"},{"id":"1058"},{"id":"1069"},{"id":"1071"},{"id":"1078"},{"id":"1086"},{"id":"1098"},{"id":"1110"},{"id":"1122"},{"id":"1132"},{"id":"1138"}],"right":[{"id":"1125"},{"id":"1141"}],"title":{"id":"1005"},"toolbar":{"id":"1026"},"toolbar_location":null,"width":1500,"x_range":{"id":"1002"},"x_scale":{"id":"1009"},"y_range":{"id":"1003"},"y_scale":{"id":"1011"}},"id":"1004","subtype":"Figure","type":"Plot"},{"attributes":{"end":200},"id":"1003","type":"Range1d"},{"attributes":{},"id":"1018","type":"BasicTicker"},{"attributes":{"formatter":{"id":"1224"},"major_label_policy":{"id":"1225"},"ticker":{"id":"1018"},"visible":false},"id":"1017","type":"LinearAxis"},{"attributes":{"dimensions":"width"},"id":"1023","type":"PanTool"},{"attributes":{},"id":"1245","type":"UnionRenderers"},{"attributes":{},"id":"1024","type":"ResetTool"},{"attributes":{},"id":"1439","type":"Selection"},{"attributes":{"end":1593},"id":"1002","type":"Range1d"},{"attributes":{},"id":"1009","type":"LinearScale"},{"attributes":{"axis":{"id":"1013"},"grid_line_color":null,"ticker":null},"id":"1016","type":"Grid"},{"attributes":{"height":15,"text":"Lollipop height:","width":200},"id":"1206","type":"Div"},{"attributes":{},"id":"1440","type":"UnionRenderers"},{"attributes":{"attachment":"below","callback":null,"point_policy":"follow_mouse","renderers":[{"id":"1042"},{"id":"1036"}],"tooltips":[["Position (compact)","@x"],["Position (chr)","@pos"],["Allele count","@allele_counts"],["Allele number","@allele_numbers"],["Allele frequency","@allele_frequencies"],["Change","@ref &gt; @alt"],["VEP Annotation","@ann"],["Severity","@sev"]]},"id":"1045","type":"HoverTool"},{"attributes":{},"id":"1246","type":"Selection"},{"attributes":{"args":{"axes":[],"plot_ls":[{"id":"1004"}],"user_line_glyphs":[{"id":"1122"}]},"code":"\n        function setVis(glyphs, vis){\n            for (let i = 0; i &lt; glyphs.length; i++){\n                if(glyphs[i] != null) { glyphs[i].visible = vis }\n            }\n        }\n        \n        function setAxisVis(vis){\n            for (let i = 0; i &lt; axes.length; i++){\n                axes[i].visible = vis\n            }\n        }\n                \n        if (cb_obj.active.includes(0)) {                \n            setVis(user_line_glyphs,true)\n            setAxisVis(true)\n        }\n        else {\n            setVis(user_line_glyphs,false)\n            setAxisVis(false)\n        }\n    "},"id":"1203","type":"CustomJS"},{"attributes":{"axis":{"id":"1017"},"dimension":1,"grid_line_color":null,"ticker":null},"id":"1020","type":"Grid"}],"root_ids":["1444"]},"title":"Bokeh Application","version":"2.3.3"}}
+        </script>
+        <script type="text/javascript">
+          (function() {
+            var fn = function() {
+              Bokeh.safely(function() {
+                (function(root) {
+                  function embed_document(root) {
+                    
+                  var docs_json = document.getElementById('2012').textContent;
+                  var render_items = [{"docid":"3b2a281c-95c7-4e9b-b079-7821b6d4f2a4","root_ids":["1444"],"roots":{"1444":"c548ba9d-37d4-4cb9-af17-e69b7a0bfe94"}}];
+                  root.Bokeh.embed.embed_items(docs_json, render_items);
+                
+                  }
+                  if (root.Bokeh !== undefined) {
+                    embed_document(root);
+                  } else {
+                    var attempts = 0;
+                    var timer = setInterval(function(root) {
+                      if (root.Bokeh !== undefined) {
+                        clearInterval(timer);
+                        embed_document(root);
+                      } else {
+                        attempts++;
+                        if (attempts > 100) {
+                          clearInterval(timer);
+                          console.log("Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing");
+                        }
+                      }
+                    }, 10, root)
+                  }
+                })(window);
+              });
+            };
+            if (document.readyState != "loading") fn();
+            else document.addEventListener("DOMContentLoaded", fn);
+          })();
+        </script>
+    
+  </body>
+  
+</html>
\ No newline at end of file
diff --git a/report/widget_callbacks.py b/report/widget_callbacks.py
new file mode 100755
index 0000000..3e8bd18
--- /dev/null
+++ b/report/widget_callbacks.py
@@ -0,0 +1,375 @@
+from bokeh.models import ColumnDataSource,CustomJS,CheckboxGroup,Legend,Slider,Div,RadioGroup
+from bokeh.plotting import figure
+from axes import format_ticks
+import numpy as np
+
+def add_linear_log_scale(axes, glyph_dict):
+    div_type = Div(text="""Lollipop height:""", width=200, height=15)
+    div_scale = Div(text="""Lollipop height scale:""", width=200, height=15)
+    
+    variant_type_labels = ['Allele count', 'Allele frequency']
+    variant_scale_labels = ['Linear', 'Log']
+    mlo_li_ct = [ax.major_label_overrides for ax in axes['count']]
+    mlo_li_fr = [ax.major_label_overrides for ax in axes['allele_frequency']]
+    
+    def log10(f): return np.log10(f) if f > 0 else 0
+    #TODO
+    mlo_lg_ct = [format_ticks({key:str(log10(float(value))) for (key,value) in d.items()}, 2, False) for d in mlo_li_ct]
+    mlo_lg_fr = [format_ticks({key:str(-log10(float(value))) for (key,value) in d.items()}, 2, False) for d in mlo_li_fr]
+
+    radio_group_type = RadioGroup(labels=variant_type_labels, active=0, width=200)
+    radio_group_scale = RadioGroup(labels=variant_scale_labels, active=0, width=200)
+    
+    radio_group_type.js_on_click(CustomJS(args=dict(radio_group_scale=radio_group_scale,axes=axes, 
+                                                    mlo_li_ct=mlo_li_ct, mlo_lg_ct=mlo_lg_ct, 
+                                                    mlo_li_fr=mlo_li_fr, mlo_lg_fr=mlo_lg_fr, 
+                                                    variant=glyph_dict['Variant']), 
+        code="""        
+        function setAxis(label, mlo){
+            for (let i = 0; i < axes['count'].length; i++){
+                axes['count'][i].axis_label = label
+                axes['count'][i].major_label_overrides = mlo[i]
+            }   
+        }
+        
+        for (let i = 0; i < variant.length; i++){
+            if (cb_obj.active == 0) {
+                if (radio_group_scale.active == 0){
+                    variant[i].data_source.data['y1_circle']=variant[i].data_source.data['y1_ci_li_ct']
+                    variant[i].data_source.data['y1_segment']=variant[i].data_source.data['y1_sg_li_ct']
+                    setAxis('Allele count', mlo_li_ct)
+                } else {
+                    variant[i].data_source.data['y1_circle']=variant[i].data_source.data['y1_ci_lg_ct']
+                    variant[i].data_source.data['y1_segment']=variant[i].data_source.data['y1_sg_lg_ct']
+                    setAxis('Log(Allele count)', mlo_lg_ct)
+                }
+            }
+            if (cb_obj.active == 1) {
+                if (radio_group_scale.active == 0){
+                    variant[i].data_source.data['y1_circle']=variant[i].data_source.data['y1_ci_li_fr']
+                    variant[i].data_source.data['y1_segment']=variant[i].data_source.data['y1_sg_li_fr']
+                    setAxis('Allele frequency', mlo_li_fr)
+                } else {
+                    variant[i].data_source.data['y1_circle']=variant[i].data_source.data['y1_ci_lg_fr']
+                    variant[i].data_source.data['y1_segment']=variant[i].data_source.data['y1_sg_lg_fr']
+                    setAxis('-Log(Allele frequency)', mlo_lg_fr)
+                }
+            }
+            variant[i].data_source.change.emit()        
+        }
+    """))    
+        
+    radio_group_scale.js_on_click(CustomJS(args=dict(radio_group_type=radio_group_type,axes=axes, 
+                                                     mlo_li_ct=mlo_li_ct, mlo_lg_ct=mlo_lg_ct, 
+                                                     mlo_li_fr=mlo_li_fr, mlo_lg_fr=mlo_lg_fr, 
+                                                     variant=glyph_dict['Variant']), code="""        
+        function setAxis(label, mlo){
+            for (let i = 0; i < axes['count'].length; i++){
+                axes['count'][i].axis_label = label
+                axes['count'][i].major_label_overrides = mlo[i]
+            }   
+        }
+        
+        for (let i = 0; i < variant.length; i++){
+            if (cb_obj.active == 0) {
+                if (radio_group_type.active == 0){
+                    variant[i].data_source.data['y1_circle']=variant[i].data_source.data['y1_ci_li_ct']
+                    variant[i].data_source.data['y1_segment']=variant[i].data_source.data['y1_sg_li_ct']
+                    setAxis('Allele count', mlo_li_ct)
+                    
+                } else {
+                    variant[i].data_source.data['y1_circle']=variant[i].data_source.data['y1_ci_li_fr']
+                    variant[i].data_source.data['y1_segment']=variant[i].data_source.data['y1_sg_li_fr']
+                    setAxis('Allele frequency', mlo_li_fr)
+                }
+            }
+            if (cb_obj.active == 1) {
+                if (radio_group_type.active == 0){
+                    variant[i].data_source.data['y1_circle']=variant[i].data_source.data['y1_ci_lg_ct']
+                    variant[i].data_source.data['y1_segment']=variant[i].data_source.data['y1_sg_lg_ct']
+                    setAxis('Log(Allele count)', mlo_lg_ct)
+                    
+                } else {
+                    variant[i].data_source.data['y1_circle']=variant[i].data_source.data['y1_ci_lg_fr']
+                    variant[i].data_source.data['y1_segment']=variant[i].data_source.data['y1_sg_lg_fr']
+                    setAxis('-Log(Allele frequency)', mlo_lg_fr)
+                    
+                }
+            }
+            variant[i].data_source.change.emit()        
+        }
+    """))    
+    
+    return div_type,radio_group_type,div_scale,radio_group_scale
+
+def add_checkbox(plot_ls, axes, glyph_dict, plot_params, variant_params):
+    labels = []
+    for tup in zip(['UTRs','Direction','Variant'], [plot_params['plot_UTRs'], plot_params['plot_direction'], variant_params['plot_variants']]):
+        if tup[1]: labels.append(tup[0])
+    active = list(range(len(labels)))
+    checkbox = CheckboxGroup(labels=labels,active=active, width=100)
+    
+    glyph_dict_checkbox = {label:glyph_dict[label] for label in labels}
+
+    callback = CustomJS(args=dict(plot_ls=plot_ls, axes=axes, labels=labels, glyph_dict_checkbox=glyph_dict_checkbox,
+                                 ), code='''
+        function setVis(glyphs, vis){
+            for (let i = 0; i < glyphs.length; i++){
+                if(glyphs[i] != null){
+                    glyphs[i].visible = vis
+                }
+            }
+        }
+        
+        function setAxisVis(axis_name, vis){
+            for (let i = 0; i < axes[axis_name].length; i++){
+                axes[axis_name][i].visible = vis
+            }
+        }
+        
+        for (let i = 0; i < labels.length; i++){
+            if (cb_obj.active.includes(i)) {setVis(glyph_dict_checkbox[labels[i]], true)}
+            else {setVis(glyph_dict_checkbox[labels[i]], false)}
+        }
+    ''')
+
+    checkbox.js_on_change('active', callback)
+    
+    return checkbox 
+
+def add_user_tracks_checkbox(plot_ls,axes,user_track_glyphs,direction_glyphs,plot_params):
+    labels = list(user_track_glyphs.keys())
+    active = list(range(len(labels)))
+    user_tracks_checkbox = CheckboxGroup(labels=labels,active=active, width=100)
+    axis_names = [ls[0].axis_label for ls in list(axes.values()) if len(ls)>0]
+    user_track_names = list(user_track_glyphs.keys())
+    
+    ori_y_coords = [user_track_glyphs[track_name][0].data_source.data['y'][0] for track_name in user_track_glyphs]
+        
+    direction_glyphs = [glyph for glyph in direction_glyphs if glyph]
+    s0_arrow = [glyph_ls.data_source for glyph_ls in direction_glyphs]
+    callback = CustomJS(args=dict(plot_ls=plot_ls, plot_params=plot_params, axis_names=axis_names,axes=axes,
+                                  user_track_glyphs=user_track_glyphs, user_track_names=user_track_names,
+                                  ori_y_coords=ori_y_coords, s0_arrow=s0_arrow
+                                 ), code='''
+        const transcript_h = plot_params['transcript_height']
+        const exon_h = plot_params['exon_height']
+        const track_h = plot_params['track_height']
+            
+        function setVis(glyphs, vis){
+            for (let i = 0; i < glyphs.length; i++){
+                if(glyphs[i] != null){
+                    glyphs[i].visible = vis
+                }
+            }
+        }
+        
+        function setAxesStart(start){
+            for (let i = 0; i < axis_names.length; i++){
+                for (let j = 0; j < plot_ls.length; j++){
+                    plot_ls[j].y_range.start = start
+                    plot_ls[j].extra_y_ranges[axis_names[i]].start = start
+                }
+            }
+        }
+        
+        //in LabelSet source is called source whereas in GlyphRenderer source is called data_source for no apparent reason
+        function get_source(glyph){
+            try {glyph.data_source.data; return glyph.data_source}
+            catch (err) {return glyph.source}
+        }
+        
+        function setY(track_name,y){
+            console.log(y)
+            for (let i = 0; i < user_track_glyphs[track_name].length; i++){
+                for (let j = 0; j < get_source(user_track_glyphs[track_name][i]).data['y'].length; j++){
+                    if (i%2==0) {get_source(user_track_glyphs[track_name][i]).data['y'][j] = y}
+                    else {get_source(user_track_glyphs[track_name][i]).data['y'][j] = y-track_h}    
+                }
+                console.log(user_track_glyphs[track_name][i])
+                get_source(user_track_glyphs[track_name][i]).change.emit()
+            }
+        }
+        
+        function adjust_arrow(s0_arrow,start){ 
+            
+            for (let i = 0; i < s0_arrow.length; i++){
+                for (let j = 0; j < s0_arrow[i].data['y'].length/2; j++){
+                    //triangle
+                    s0_arrow[i].data['y'][j*2+1][0][0][0] = transcript_h-exon_h/2 + start/(track_h*1.5) //start 57
+                    s0_arrow[i].data['y'][j*2+1][0][0][1] = transcript_h+exon_h/2 - start/(track_h*1.5)
+                    //rectangle
+                    s0_arrow[i].data['y'][j*2][0][0][0] = transcript_h-exon_h/5 + start/(track_h*1.5*3)
+                    s0_arrow[i].data['y'][j*2][0][0][1] = transcript_h+exon_h/5 - start/(track_h*1.5*3)
+                    s0_arrow[i].data['y'][j*2][0][0][2] = transcript_h+exon_h/5 - start/(track_h*1.5*3)
+                    s0_arrow[i].data['y'][j*2][0][0][3] = transcript_h-exon_h/5 + start/(track_h*1.5*3)
+                }
+                s0_arrow[i].change.emit()
+            }
+        }
+        
+        var temp = 0
+        var y_co = 0
+        
+        for (let i = 0; i < user_track_names.length; i++){
+            if (cb_obj.active.includes(i)) {
+                setVis(user_track_glyphs[user_track_names[i]],true)
+                setY(user_track_names[i], ori_y_coords[temp])
+                y_co = ori_y_coords[temp]
+                temp++
+            }
+            else {setVis(user_track_glyphs[user_track_names[i]],false)}
+        }
+        var start = 0
+        if (y_co==0){start = plot_params['transcript_height']-plot_params['exon_height']/2}
+        else {start = y_co-ori_y_coords[ori_y_coords.length-1]}
+        setAxesStart(start)
+        adjust_arrow(s0_arrow,start)
+    ''')
+
+    user_tracks_checkbox.js_on_change('active', callback)
+    return user_tracks_checkbox
+
+def add_user_lines_checkbox(plot_ls,axis,user_line_glyphs,label):
+    user_lines_checkbox = CheckboxGroup(labels=[label],active=[0], width=100, align=('start','center'))
+    callback = CustomJS(args=dict(plot_ls=plot_ls, axes=axis,
+                                  user_line_glyphs=user_line_glyphs
+                                 ), code='''
+        function setVis(glyphs, vis){
+            for (let i = 0; i < glyphs.length; i++){
+                if(glyphs[i] != null) { glyphs[i].visible = vis }
+            }
+        }
+        
+        function setAxisVis(vis){
+            for (let i = 0; i < axes.length; i++){
+                axes[i].visible = vis
+            }
+        }
+                
+        if (cb_obj.active.includes(0)) {                
+            setVis(user_line_glyphs,true)
+            setAxisVis(true)
+        }
+        else {
+            setVis(user_line_glyphs,false)
+            setAxisVis(false)
+        }
+    ''')
+
+    user_lines_checkbox.js_on_change('active', callback)
+    return user_lines_checkbox
+
+def add_smoothing_slider(glyph_ls, fill_area_ls, title=''):
+    slider = Slider(start=1, end=100, value=25, step=1, title=title, width=250)
+    slider = Slider(start=1, end=100, value=1, step=1, title=title, width=250)
+    slider.js_on_change("value", CustomJS(args=dict(glyph_ls=glyph_ls, fill_area_ls=fill_area_ls),code="""
+        function smooth(y,k,fill_area) {
+            //console.log(fill_area)
+            var smoothed_ls = [ ... y]
+            if (smoothed_ls.length <= 2) {return smoothed_ls}
+            if (fill_area) {smoothed_ls = smoothed_ls.slice(1,smoothed_ls.length-1)}
+            
+            for (let i = 0; i < smoothed_ls.length; i += k){
+                const window_avg = mean(smoothed_ls.slice(i, i+k))
+                for (let j = i; j < i + k; j++){
+                    if (j < smoothed_ls.length-1) { smoothed_ls[j] = window_avg }
+                }
+            }
+            if (fill_area) {return [y[0], ...smoothed_ls, y[y.length-1]]}
+            
+            else {return smoothed_ls}
+        }
+        
+        function mean(y) { return y.reduce((i, j) => i + j) / y.length }
+        
+        console.log(glyph_ls)
+        for (let i = 0; i < glyph_ls.length; i++){
+            //console.log(fill_area_ls[i])
+            for (let j = 0; j < glyph_ls[i].data_source.data['y'].length; j++){
+                glyph_ls[i].data_source.data['y'][j] = smooth(glyph_ls[i].data_source.data['y_unsmoothed'][j], cb_obj.value, fill_area_ls[i])
+            }
+            glyph_ls[i].data_source.change.emit()
+        }
+        
+    """))
+    return slider
+
+
+def add_legend(user_line_params, height=70, width=270):
+    num_lines = sum([len(user_line_params[axis_name]['lines']) for axis_name in user_line_params])
+    #legend_plot = figure(plot_height=height,plot_width=width,toolbar_location=None)
+    legend_plot = figure(plot_height=30*num_lines,plot_width=width,toolbar_location=None)
+    legend_plot.yaxis.visible = legend_plot.xaxis.visible = legend_plot.grid.visible = False
+    
+    legend_items = []
+    for axis_name in user_line_params:
+        for line in user_line_params[axis_name]['lines']:        
+        #TODO add alpha?
+            legend_glyph = legend_plot.line(x=[0,1],y=[0,1],line_color=user_line_params[axis_name]['lines'][line]['color'])
+            legend_items.append((line, [legend_glyph]))
+            legend_glyph.visible = False
+
+    legend = Legend(items=legend_items, location=(0,0))
+    legend_plot.add_layout(legend, 'center')
+    legend_plot.legend.label_text_font_size = '12px'
+    
+    return legend_plot
+
+def add_exon_zoom(plot_ls,glyph_dict):
+    for (plot,exon_glyph,arrow_glyph) in zip(plot_ls,glyph_dict['exon'], glyph_dict['Direction']):
+        s0_exon = exon_glyph.data_source
+        s1_exon = ColumnDataSource(data=exon_glyph.data_source.data) #deep copy is not working in CustomJS so I'm doing it here
+        try:
+            s0_arrow = arrow_glyph.data_source
+            s1_arrow = ColumnDataSource(data=arrow_glyph.data_source.data)
+        except: s0_arrow = s1_arrow = None
+
+        callback = CustomJS(args=dict(plot=plot, s0_exon=s0_exon, s1_exon=s1_exon, 
+                                  s0_arrow=s0_arrow, s1_arrow=s1_arrow,
+                       ),code="""
+        cb_obj.active = !cb_obj.active
+        const N_exon = s1_exon.data['x'].length
+        const idx = cb_obj.indices[0]
+        const active_exon_start = s1_exon.data['adj_start'][idx]
+        const active_exon_end = s1_exon.data['adj_end'][idx]
+        const active_exon_len = s1_exon.data['true_len'][idx]
+        const plot_len = plot.x_range.end
+        
+        function adjust_arrow(s0_arrow, s1_arrow){
+            const N_arrow = s1_arrow.data['x'].length/2
+            var direc_int = 1
+            if (s1_arrow.data['direction'][idx*2] == '-') {direc_int = -1}
+            const plot_mdpt = active_exon_start + active_exon_len/2
+            s0_arrow.data['x'][idx*2][0][0] = [-3, -3, 0, 0].map(function(x) { return x * direc_int * active_exon_len / 200 + plot_mdpt; })
+            s0_arrow.data['x'][idx*2+1][0][0] = [0,0,3].map(function(x) { return x * direc_int * active_exon_len / 200 + plot_mdpt; })
+        }
+        
+        function reset_arrow(s0_arrow, s1_arrow){
+            const N_arrow = s1_arrow.data['x'].length
+            for (let i = 0; i < N_arrow; i++){
+                s0_arrow.data['x'][i][0][0] = s1_arrow.data['x'][i][0][0]
+            }
+        }
+        
+        function adjust_x_axis() {
+            plot.x_range.start = active_exon_start
+            plot.x_range.end = active_exon_end
+        }
+        
+        function reset_x_axis() {
+            plot.x_range.start = 0
+            plot.x_range.end = s1_exon.data['adj_end'][N_exon-1]
+        }
+                       
+        if(cb_obj.active){
+            adjust_x_axis()
+            if (s1_arrow != null) {adjust_arrow(s0_arrow, s1_arrow)}
+        } else{
+            reset_x_axis()
+            if (s1_arrow != null) {reset_arrow(s0_arrow, s1_arrow)}
+        }
+        if (s1_arrow != null) {s0_arrow.change.emit()}
+    """)
+
+        s0_exon.selected.js_on_change('indices', callback)

From ee3b242dae50a7db2bfa328f1b856b32b93d0e7d Mon Sep 17 00:00:00 2001
From: Suchita Lulla <suchitalulla@gmail.com>
Date: Wed, 27 Oct 2021 19:29:32 -0600
Subject: [PATCH 2/9] added create_constraint_txt functionality

---
 report/constraintview.py        | 63 ++-------------------------------
 report/create_constraint_txt.py | 46 ++++++++++++++++++++++++
 report/process_gene_gff.py      | 62 ++++++++++++++++++++++++++++++++
 3 files changed, 110 insertions(+), 61 deletions(-)
 create mode 100644 report/create_constraint_txt.py
 create mode 100644 report/process_gene_gff.py

diff --git a/report/constraintview.py b/report/constraintview.py
index 78c540f..d9a756f 100755
--- a/report/constraintview.py
+++ b/report/constraintview.py
@@ -1,3 +1,4 @@
+from process_gene_gff import gff_to_db, get_gene_feature, get_transcript_dict
 from get_coords import get_variants,get_line,get_track
 from map_coords import map_line
 from colors import color_boxes, color_variants
@@ -5,7 +6,6 @@
 from glyphs import add_intron_glyph, add_exon_glyph, add_variant_glyph, add_UTR_glyph, add_track_glyph, add_multi_line_glyph
 from widget_callbacks import add_checkbox,add_user_tracks_checkbox,add_user_lines_checkbox,add_smoothing_slider,add_legend,add_linear_log_scale,add_exon_zoom
 import project_coords
-import gffutils
 import numpy as np
 import argparse
 from bokeh.plotting import figure, output_file, save
@@ -15,66 +15,6 @@
 import yaml
 from yaml.loader import SafeLoader
 
-def get_gene_feature(gff_db, gene_name):
-    #get ID from name
-    for f in gff_db.all_features(featuretype='gene'):
-        try:
-            if gene_name in f['Name'][0]: return f
-        except: continue
-    raise ValueError('No gene with name {}'.format(gene_name))
-    
-def get_transcript_dict(plot_params, gff_db, gene_feature, transcript_IDs):
-    chr_num = gene_feature.seqid
-    print(chr_num)
-    transcript_dict = {}
-
-    #get all exons and flatten
-    if 'flattened-exons' in transcript_IDs or transcript_IDs=='all':
-        exons_all = gff_db.children(gene_feature, featuretype='exon')
-        exons_all = [{'start': e.start, 'end': e.end} for e in exons_all]
-        exons_all = project_coords.flatten_exons(exons_all)
-        transcript_dict['flattened-exons'] = dict(ID='flattened_exons', chr_num=chr_num, exons=exons_all,
-                                                  direction='', UTRs=[])    
-        
-    def get_UTRs(transcript):
-        if not plot_params['plot_UTRs']: return []
-        UTRs = []
-        for f in ['five_prime_UTR', 'three_prime_UTR']:
-            try:
-                UTR = list(gff_db.children(transcript, featuretype=f))
-                if len(UTR) > 1: 
-                    print('Warning: transcript {} has {} {} annotations; using first annotation.'.format(tname, len(UTR), featuretype))
-                UTR_dict = {'featuretype': f, 'start': UTR[0].start, 'end': UTR[0].end}
-                UTRs.append(UTR_dict)
-            except: continue 
-        return UTRs
-                
-    #indiv mRNAs
-    transcripts = list(gff_db.children(gene_feature, featuretype='mRNA'))
-    if transcript_IDs != 'all':
-        for ID in transcript_IDs:
-            if ID not in [t['Name'][0] for t in transcripts]: print('No such transcript {}; skipping'.format(ID))
-        transcripts = [t for t in transcripts if t['Name'][0] in transcript_IDs]
-        #print([t['ID'] for t in transcripts])
-
-    for t in transcripts:
-        exons = list(gff_db.children(t, featuretype='exon'))
-        exon_coords = [{'start': e.start, 'end': e.end, 'compact_start': -1, 'compact_end': -1} for e in exons]
-        direction = t.strand if plot_params['plot_direction'] else ''
-        tname = t['Name'][0]
-        UTRs = get_UTRs(t)
-        transcript_dict[tname] = dict(ID=t['ID'], chr_num=chr_num, exons=exon_coords, direction=direction, 
-                                UTRs=UTRs)
-    return transcript_dict
-
-def gff_to_db(gff_path,output_name):
-    try:
-        db = gffutils.FeatureDB(gff_path, keep_order=True)
-    except:
-        gffutils.create_db(gff_path, dbfn=output_name, force=True, keep_order=True, merge_strategy='merge', sort_attribute_values=True)
-        db = gffutils.FeatureDB(gff_path, keep_order=True)
-    return db
-
 def constraint_view_plot(plot_params, variant_params, user_line_params, transcript_dict, glyph_dict, axes, variant_ls, user_tracks, user_track_glyphs, user_lines, user_line_glyphs, title=''):
     project_coords.adjust_coordinates(transcript_dict['exons'], intron_size=plot_params['intron_size'])
     plot_height = plot_params['plot_height']    
@@ -215,6 +155,7 @@ def constraint_view():
     gff_db = gff_to_db(plot_params['gff_path'],plot_params['gff_path']+'test.db')
     
     gene_feature = get_gene_feature(gff_db, plot_params['gene_name'])
+    #print(gene_feature.start)
 
     if transcript_IDs == 'transcript_names':
         transcripts = get_transcript_dict(plot_params, gff_db, gene_feature, 'all')
diff --git a/report/create_constraint_txt.py b/report/create_constraint_txt.py
new file mode 100644
index 0000000..ded45ed
--- /dev/null
+++ b/report/create_constraint_txt.py
@@ -0,0 +1,46 @@
+import argparse
+import sys
+sys.path.append("../utilities")
+sys.path.append("../predict-constraint")
+
+from compute_mutation_counts import compute_mutation_counts
+from process_gene_gff import gff_to_db,get_gene_feature
+
+def create_constraint_txt(gene_start, gene_end, chr_num, model, expected_out_filepath='expected_mut_counts.txt-1', observed_out_filepath='observed_mut_counts.txt-1', window_size=51, window_stride=25):
+    exp_fi = open(expected_out_filepath, 'w')
+    obs_fi = open(observed_out_filepath, 'w')
+    
+    #mutation_dict = compute_mutation_counts('chr{}:{}-{}'.format(chr_num,gene_start,gene_end), model, window_size, window_stride)
+    #mutation_dict = compute_mutation_counts('{}:{}-{}'.format(chr_num,gene_start,gene_end), model, window_size, window_stride)
+    compute_mutation_counts('chr1:100,000-100,100', model, window_size, window_stride)
+    
+    xs = mutation_dict['windowPositions']
+    y1s = mutation_dict['windowExpectedMutationCounts']
+    y2s = mutation_dict['windowObservedMutationCounts']
+
+    for (x,y) in list(zip(xs,y1s)): exp_fi.write('{}\t{}\t{}\n'.format(chr_num,x,y))
+    for (x,y) in list(zip(xs,y2s)): obs_fi.write('{}\t{}\t{}\n'.format(chr_num,x,y))
+
+    exp_fi.close()
+    obs_fi.close()
+
+parser = argparse.ArgumentParser(description='create_constraint_txt')
+parser.add_argument('gff_path')
+parser.add_argument('model_path')
+parser.add_argument('gene_name')
+parser.add_argument('seqid')
+parser.add_argument('-o', '--output', required=False)
+args = parser.parse_args()
+
+
+#gff_db = gff_to_db(plot_params['gff_path'],plot_params['gff_path']+'test.db')
+# 'test.db' to make sure .db does not get overwritten during development    
+gff_db = gff_to_db(args.gff_path, args.gff_path + 'test.db')
+#tmp = '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/Homo_sapiens.GRCh38.104.gff3.db'
+#gff_db = gff_to_db(tmp, tmp+'test.db')
+
+#gene_feature = get_gene_feature(gff_db, plot_params['gene_name'])
+gene_feature = get_gene_feature(gff_db, args.gene_name)
+
+#TODO maybe make this a config file
+create_constraint_txt(gene_feature.start, gene_feature.end, args.seqid, args.model_path, expected_out_filepath='expected_mut_counts.txt', observed_out_filepath='observed_mut_counts.txt', window_size=51, window_stride=25)
\ No newline at end of file
diff --git a/report/process_gene_gff.py b/report/process_gene_gff.py
new file mode 100644
index 0000000..c28f74f
--- /dev/null
+++ b/report/process_gene_gff.py
@@ -0,0 +1,62 @@
+import gffutils
+
+def gff_to_db(gff_path,output_name):
+    try:
+        db = gffutils.FeatureDB(gff_path, keep_order=True)
+    except:
+        gffutils.create_db(gff_path, dbfn=output_name, force=True, keep_order=True, merge_strategy='merge', sort_attribute_values=True)
+        db = gffutils.FeatureDB(gff_path, keep_order=True)
+    return db
+
+def get_gene_feature(gff_db, gene_name):
+    #get ID from name
+    for f in gff_db.all_features(featuretype='gene'):
+        try:
+            if gene_name in f['Name'][0]: return f
+        except: continue
+    raise ValueError('No gene with name {}'.format(gene_name))
+
+def get_transcript_dict(plot_params, gff_db, gene_feature, transcript_IDs):
+    chr_num = gene_feature.seqid
+    print(chr_num)
+    transcript_dict = {}
+
+    #get all exons and flatten
+    if 'flattened-exons' in transcript_IDs or transcript_IDs=='all':
+        exons_all = gff_db.children(gene_feature, featuretype='exon')
+        exons_all = [{'start': e.start, 'end': e.end} for e in exons_all]
+        exons_all = project_coords.flatten_exons(exons_all)
+        transcript_dict['flattened-exons'] = dict(ID='flattened_exons', chr_num=chr_num, exons=exons_all,
+                                                  direction='', UTRs=[])    
+        
+    def get_UTRs(transcript):
+        if not plot_params['plot_UTRs']: return []
+        UTRs = []
+        for f in ['five_prime_UTR', 'three_prime_UTR']:
+            try:
+                UTR = list(gff_db.children(transcript, featuretype=f))
+                if len(UTR) > 1: 
+                    print('Warning: transcript {} has {} {} annotations; using first annotation.'.format(tname, len(UTR), featuretype))
+                UTR_dict = {'featuretype': f, 'start': UTR[0].start, 'end': UTR[0].end}
+                UTRs.append(UTR_dict)
+            except: continue 
+        return UTRs
+                
+    #indiv mRNAs
+    transcripts = list(gff_db.children(gene_feature, featuretype='mRNA'))
+    if transcript_IDs != 'all':
+        for ID in transcript_IDs:
+            if ID not in [t['Name'][0] for t in transcripts]: print('No such transcript {}; skipping'.format(ID))
+        transcripts = [t for t in transcripts if t['Name'][0] in transcript_IDs]
+        #print([t['ID'] for t in transcripts])
+
+    for t in transcripts:
+        exons = list(gff_db.children(t, featuretype='exon'))
+        exon_coords = [{'start': e.start, 'end': e.end, 'compact_start': -1, 'compact_end': -1} for e in exons]
+        direction = t.strand if plot_params['plot_direction'] else ''
+        tname = t['Name'][0]
+        UTRs = get_UTRs(t)
+        transcript_dict[tname] = dict(ID=t['ID'], chr_num=chr_num, exons=exon_coords, direction=direction, 
+                                UTRs=UTRs)
+    return transcript_dict
+

From 1074771f5c5ceeeddd5a07860a0594890dc16692 Mon Sep 17 00:00:00 2001
From: Suchita Lulla <suchitalulla@gmail.com>
Date: Mon, 1 Nov 2021 16:38:11 -0600
Subject: [PATCH 3/9] updated cmc, modified fetch_SNVs for new model, added
 report as tool

---
 constraint-tools                |    4 +-
 report/constraintview           |   23 +
 report/constraintview.py        |    1 +
 report/constraintview.yaml      |    3 +-
 report/create_constraint_txt.py |   40 +-
 report/expected_mut_counts.txt  | 5798 +++++++++++++++----------------
 report/observed_mut_counts.txt  | 5798 +++++++++++++++----------------
 report/plot.html                |    6 +-
 report/process_gene_gff.py      |    2 +-
 utilities/fetch_SNVs.py         |   94 +-
 utilities/fetch_SNVs_old.py     |   89 +
 11 files changed, 6003 insertions(+), 5855 deletions(-)
 create mode 100755 report/constraintview
 mode change 100755 => 100644 report/expected_mut_counts.txt
 mode change 100755 => 100644 report/observed_mut_counts.txt
 create mode 100644 utilities/fetch_SNVs_old.py

diff --git a/constraint-tools b/constraint-tools
index 54556be..bae0bc9 100755
--- a/constraint-tools
+++ b/constraint-tools
@@ -23,9 +23,9 @@ export PYTHONPATH="${CONSTRAINT_TOOLS}/utilities:${CONSTRAINT_TOOLS}/predict-con
 PATH="${CONSTRAINT_TOOLS}/bin:$PATH" 
 PATH="${CONSTRAINT_TOOLS}/train-model:$PATH" 
 PATH="${CONSTRAINT_TOOLS}/flask-app:${PATH}"
+PATH="${CONSTRAINT_TOOLS}/report:${PATH}"
 
 #######################################
-
 tool="${1}"
 info "\nTool: ${tool}\n"
 shift
@@ -36,6 +36,8 @@ if [[ ${tool} == "train" ]]; then
   train-model ${args}
 elif [[ ${tool} == "dashboard" ]]; then 
   flask-app ${args} 
+elif [[ ${tool} == "report" ]]; then 
+  constraintview ${args}
 else
   error "invalid tool: ${tool}"
   exit 1
diff --git a/report/constraintview b/report/constraintview
new file mode 100755
index 0000000..d4c10b9
--- /dev/null
+++ b/report/constraintview
@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+###args: gff_path, model_path, gene_name, seqid (create)
+#config file, transcripts, outputfile (opt)
+
+config_file="constraintview.yaml"
+#transcripts="all"
+output="plot.html"
+
+while [[ "$1" =~ ^- ]]; do 
+  case $1 in
+    --config_file ) shift; [[ ! $1 =~ ^- ]] && config_file=$1;;
+    --transcripts ) shift; [[ ! $1 =~ ^- ]] && transcripts=$1;;
+    --output ) shift; [[ ! $1 =~ ^- ]] && output=$1;;
+    *) error "$0: $1 is an invalid flag"; exit 1;;
+  esac 
+  shift
+done
+
+echo ${transcripts}
+
+cd ${CONSTRAINT_TOOLS}/report
+python create_constraint_txt.py constraintview.yaml
+python constraintview.py ${config_file} ${transcripts} -o ${output}
\ No newline at end of file
diff --git a/report/constraintview.py b/report/constraintview.py
index d9a756f..ddde395 100755
--- a/report/constraintview.py
+++ b/report/constraintview.py
@@ -108,6 +108,7 @@ def parse_args():
 
     ###CONFIG###
     config_file = args.config_file
+    print(config_file)
     # TODO what to do if config file doesn't have required params?
     if config_file[-5:] != '.yaml': raise ValueError('configuration file must be .yaml')
     with open(config_file) as f:
diff --git a/report/constraintview.yaml b/report/constraintview.yaml
index 51230f2..bc13d98 100755
--- a/report/constraintview.yaml
+++ b/report/constraintview.yaml
@@ -8,9 +8,10 @@
 gff_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/Homo_sapiens.GRCh38.104.gff3.db'
 variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomAD_v3.1.1_ENSG00000075043_2021_09_16_16_02_28.csv'
 #variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomad.exomes.r2.1.1.sites.20.vcf.bgz'
-model_path : '/uufs/chpc.utah.edu/common/HIPAA/u6038618/constraint-tools/test-model/model-new-modified.json'
+model_path: '/scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/model.ptm.json' 
 ####Plot params
 gene_name: 'KCNQ2'
+seqid: chr20
 
 plot_height: 200
 plot_width: 1500
diff --git a/report/create_constraint_txt.py b/report/create_constraint_txt.py
index ded45ed..bd33998 100644
--- a/report/create_constraint_txt.py
+++ b/report/create_constraint_txt.py
@@ -1,4 +1,6 @@
 import argparse
+import yaml
+from yaml.loader import SafeLoader
 import sys
 sys.path.append("../utilities")
 sys.path.append("../predict-constraint")
@@ -6,14 +8,13 @@
 from compute_mutation_counts import compute_mutation_counts
 from process_gene_gff import gff_to_db,get_gene_feature
 
-def create_constraint_txt(gene_start, gene_end, chr_num, model, expected_out_filepath='expected_mut_counts.txt-1', observed_out_filepath='observed_mut_counts.txt-1', window_size=51, window_stride=25):
+#def create_constraint_txt(gene_start, gene_end, chr_num, model, expected_out_filepath='expected_mut_counts.txt', observed_out_filepath='observed_mut_counts.txt', window_size=51, window_stride=25):
+
+def create_constraint_txt(gene_start, gene_end, chr_num, model, expected_out_filepath='expected_mut_counts.txt', observed_out_filepath='observed_mut_counts.txt', window_size=51, window_stride=25):
     exp_fi = open(expected_out_filepath, 'w')
     obs_fi = open(observed_out_filepath, 'w')
     
-    #mutation_dict = compute_mutation_counts('chr{}:{}-{}'.format(chr_num,gene_start,gene_end), model, window_size, window_stride)
-    #mutation_dict = compute_mutation_counts('{}:{}-{}'.format(chr_num,gene_start,gene_end), model, window_size, window_stride)
-    compute_mutation_counts('chr1:100,000-100,100', model, window_size, window_stride)
-    
+    mutation_dict = compute_mutation_counts('{}:{}-{}'.format(chr_num,gene_start,gene_end), model, window_size, window_stride)
     xs = mutation_dict['windowPositions']
     y1s = mutation_dict['windowExpectedMutationCounts']
     y2s = mutation_dict['windowObservedMutationCounts']
@@ -24,23 +25,30 @@ def create_constraint_txt(gene_start, gene_end, chr_num, model, expected_out_fil
     exp_fi.close()
     obs_fi.close()
 
+# parser = argparse.ArgumentParser(description='create_constraint_txt')
+# parser.add_argument('gff_path')
+# parser.add_argument('model_path')
+# parser.add_argument('gene_name')
+# parser.add_argument('seqid')
 parser = argparse.ArgumentParser(description='create_constraint_txt')
-parser.add_argument('gff_path')
-parser.add_argument('model_path')
-parser.add_argument('gene_name')
-parser.add_argument('seqid')
-parser.add_argument('-o', '--output', required=False)
+parser.add_argument('config_file')
 args = parser.parse_args()
 
+with open(args.config_file) as f:
+    params = list(yaml.load_all(f, Loader=SafeLoader))
+    plot_params = params[0]
+
 
-#gff_db = gff_to_db(plot_params['gff_path'],plot_params['gff_path']+'test.db')
 # 'test.db' to make sure .db does not get overwritten during development    
-gff_db = gff_to_db(args.gff_path, args.gff_path + 'test.db')
+#gff_db = gff_to_db(args.gff_path, args.gff_path + 'test.db')
+gff_db = gff_to_db(plot_params['gff_path'], plot_params['gff_path'] + 'test.db')
 #tmp = '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/Homo_sapiens.GRCh38.104.gff3.db'
-#gff_db = gff_to_db(tmp, tmp+'test.db')
 
-#gene_feature = get_gene_feature(gff_db, plot_params['gene_name'])
-gene_feature = get_gene_feature(gff_db, args.gene_name)
+gene_feature = get_gene_feature(gff_db, plot_params['gene_name'])
+#gene_feature = get_gene_feature(gff_db, args.gene_name)
 
 #TODO maybe make this a config file
-create_constraint_txt(gene_feature.start, gene_feature.end, args.seqid, args.model_path, expected_out_filepath='expected_mut_counts.txt', observed_out_filepath='observed_mut_counts.txt', window_size=51, window_stride=25)
\ No newline at end of file
+#create_constraint_txt(gene_feature.start, gene_feature.end, args.seqid, args.model_path, expected_out_filepath='expected_mut_counts.txt', observed_out_filepath='observed_mut_counts.txt', window_size=51, window_stride=25)
+create_constraint_txt(gene_feature.start, gene_feature.end, plot_params['seqid'], plot_params['model_path'], expected_out_filepath='expected_mut_counts.txt', observed_out_filepath='observed_mut_counts.txt', window_size=51, window_stride=25)
+
+#python create_constraint_txt.py '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/Homo_sapiens.GRCh38.104.gff3.db' /scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/model.ptm.json KCNQ2 chr20
\ No newline at end of file
diff --git a/report/expected_mut_counts.txt b/report/expected_mut_counts.txt
old mode 100755
new mode 100644
index c418e72..dd1cb79
--- a/report/expected_mut_counts.txt
+++ b/report/expected_mut_counts.txt
@@ -1,2899 +1,2899 @@
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diff --git a/report/observed_mut_counts.txt b/report/observed_mut_counts.txt
old mode 100755
new mode 100644
index c0845a1..ff8602a
--- a/report/observed_mut_counts.txt
+++ b/report/observed_mut_counts.txt
@@ -1,2899 +1,2899 @@
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diff --git a/report/plot.html b/report/plot.html
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         </script>
         <script type="text/javascript">
           (function() {
@@ -52,7 +52,7 @@
                   function embed_document(root) {
                     
                   var docs_json = document.getElementById('2012').textContent;
-                  var render_items = [{"docid":"5b149a0c-f4fc-4032-8e69-f9b5836395e6","root_ids":["1444"],"roots":{"1444":"bcc27f88-2ef3-4727-bff2-42e44163964b"}}];
+                  var render_items = [{"docid":"3214713b-8250-4154-a123-b5eebf11f792","root_ids":["1444"],"roots":{"1444":"45ea8eef-9080-4f94-ad31-06a404db5be1"}}];
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diff --git a/report/process_gene_gff.py b/report/process_gene_gff.py
index c28f74f..8d2cfcf 100644
--- a/report/process_gene_gff.py
+++ b/report/process_gene_gff.py
@@ -1,4 +1,5 @@
 import gffutils
+import project_coords
 
 def gff_to_db(gff_path,output_name):
     try:
@@ -18,7 +19,6 @@ def get_gene_feature(gff_db, gene_name):
 
 def get_transcript_dict(plot_params, gff_db, gene_feature, transcript_IDs):
     chr_num = gene_feature.seqid
-    print(chr_num)
     transcript_dict = {}
 
     #get all exons and flatten
diff --git a/utilities/fetch_SNVs.py b/utilities/fetch_SNVs.py
index a01d467..a37496b 100644
--- a/utilities/fetch_SNVs.py
+++ b/utilities/fetch_SNVs.py
@@ -7,19 +7,25 @@
 from kmer import fetch_kmer_from_genome, fetch_kmer_from_sequence, middle_base, middle_index, check_for_Ns
 
 def fetch_SNVs(mutations, genome, region, meta):
+  #mutations = "/scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/gnomad/v3/gnomad_v3_variants.sorted.bed.gz "
+  #mutations = "/scratch/ucgd/lustre-work/quinlan/u6018199/constraint-tools/data/icgc/mutations.sorted.maf.gz"
+  #print(mutations)
   SNVs = []
   column_headings = [
-    'Chromosome'.lower(), 
-    'Start_Position'.lower(),
-    'End_Position'.lower(),
-    'Reference_Allele'.lower(), 
-    'Tumor_Seq_Allele1'.lower(), 
-    'Tumor_Seq_Allele2'.lower(), 
-    'Tumor_Sample_Barcode'.lower(),
-    'Variant_Type'.lower(), 
-    'ref_context' 
+    #'Chromosome'.lower(), 
+    #'Start_Position'.lower(),
+    #'End_Position'.lower(),
+    #'Reference_Allele'.lower(), 
+    #'Tumor_Seq_Allele1'.lower(), 
+    #'Tumor_Seq_Allele2'.lower(), 
+    #'Tumor_Sample_Barcode'.lower(),
+    #'Variant_Type'.lower(), 
+    #'ref_context' 
+    'chrom', 'start', 'end', 'ref', 'alt', 'allele_count', 'variant_type'
   ]
   column_heading_indices = fetch_column_heading_indices(meta['mutations'])
+  #print('a')
+  #print('column_heading_indices',column_heading_indices)
   for row in mutations.fetch(region=region, parser=pysam.asTuple()):
     mutation = {}
     for column_heading in column_headings: 
@@ -27,39 +33,53 @@ def fetch_SNVs(mutations, genome, region, meta):
         mutation[column_heading] = row[column_heading_indices[column_heading]]
       except KeyError: 
         continue
+    #if mutation['reference_allele'] == '-': continue # exclude INS
+    #print(mutation['start'])
+    if mutation['ref'] == '-': continue # exclude INS
+    #if len(mutation['reference_allele']) != 1: continue # exclude DEL, DNP, TNP, ONP
+    if len(mutation['ref']) != 1: continue
+    #if mutation['tumor_seq_allele2'] not in {'A', 'T', 'G', 'C'}: continue # exclude DEL
+    if mutation['alt'] not in {'A', 'T', 'G', 'C'}: continue
+    
+    ###I don't think we need this block???
+    #try: 
+      #if mutation['reference_allele'] != mutation['tumor_seq_allele1']: # sanity check
+    #    print_json(mutation)
+    #    raise ValueError('Tumor allele 1 is not the same as reference allele') 
+    #  del mutation['tumor_seq_allele1']
+    #except KeyError:
+    #  pass
 
-    if mutation['reference_allele'] == '-': continue # exclude INS
-    if len(mutation['reference_allele']) != 1: continue # exclude DEL, DNP, TNP, ONP
-    if mutation['tumor_seq_allele2'] not in {'A', 'T', 'G', 'C'}: continue # exclude DEL 
-
-    try: 
-      if mutation['reference_allele'] != mutation['tumor_seq_allele1']: # sanity check
-        print_json(mutation)
-        raise ValueError('Tumor allele 1 is not the same as reference allele') 
-      del mutation['tumor_seq_allele1']
-    except KeyError:
-      pass
-
-    start = int(mutation['start_position'])
-    mutation['position'] = start - 1
-    del mutation['start_position']
+    #start = int(mutation['start_position'])
+    start = int(mutation['start'])
+    #mutation['position'] = start - 1
+    mutation['position'] = start
+    #del mutation['start_position']
+    del mutation['start']
 
     try: 
-      if start != int(mutation['end_position']): # sanity check for SNPs
+      #if start != int(mutation['end_position']): # sanity check for SNPs
+      if start != int(mutation['end'])-1: # sanity check for SNPs
         print_json(mutation)
-        raise ValueError('SNPs must have equal start and end values') 
-      del mutation['end_position']
+        #raise ValueError('SNPs must have equal start and end values') 
+        raise ValueError('SNPs must start and end values 1 bp apart') 
+      #del mutation['end_position']
+      del mutation['end']
     except KeyError:
       pass
 
-    kmer = fetch_kmer_from_genome(genome, mutation['chromosome'], mutation['position'], meta['kmer_size'])
+    #kmer = fetch_kmer_from_genome(genome, mutation['chromosome'], mutation['position'], meta['kmer_size'])
+    kmer = fetch_kmer_from_genome(genome, mutation['chrom'], mutation['position'], meta['kmer_size'])
     mutation['kmer'] = kmer
     
-    if middle_base(kmer) != mutation['reference_allele'].upper(): # sanity check
+    #if middle_base(kmer) != mutation['reference_allele'].upper(): # sanity check
+    if middle_base(kmer) != mutation['ref'].upper(): # sanity check
       print_json(mutation)
-      raise ValueError('Middle base of kmer does not match ref allele: {} {}'.format(
+      raise ValueError('Middle base of kmer does not match ref allele: {} {} {}'.format(
         middle_base(kmer), 
-        mutation['reference_allele']
+        kmer,
+        #mutation['reference_allele']
+        mutation['ref']
       )) 
     
     try:
@@ -74,15 +94,19 @@ def fetch_SNVs(mutations, genome, region, meta):
       pass
 
     try: 
-      if mutation['variant_type'] != 'SNP': # sanity check
+      #if mutation['variant_type'] != 'SNP': # sanity check
+      if mutation['feature_type'] != 'SNP': # sanity check
         print_json(mutation)
         raise ValueError('variant_type is not SNP') 
-      del mutation['variant_type']
+      #del mutation['variant_type']
+      del mutation['feature_type']
     except KeyError:
       pass
 
-    mutation['REF'] = mutation.pop('reference_allele')
-    mutation['ALT'] = mutation.pop('tumor_seq_allele2')
+    #mutation['REF'] = mutation.pop('reference_allele')
+    mutation['REF'] = mutation.pop('ref')
+    #mutation['ALT'] = mutation.pop('tumor_seq_allele2')
+    mutation['ALT'] = mutation.pop('alt')
 
     SNVs.append(mutation)
   return SNVs
diff --git a/utilities/fetch_SNVs_old.py b/utilities/fetch_SNVs_old.py
new file mode 100644
index 0000000..a01d467
--- /dev/null
+++ b/utilities/fetch_SNVs_old.py
@@ -0,0 +1,89 @@
+# pysam API: 
+# https://github.com/pysam-developers/pysam/blob/b82cbcae22c088e64fdb58f8acaf1e9773c7b088/pysam/libctabix.pyx
+import pysam
+
+from column_headings import fetch_column_heading_indices
+from colorize import print_json
+from kmer import fetch_kmer_from_genome, fetch_kmer_from_sequence, middle_base, middle_index, check_for_Ns
+
+def fetch_SNVs(mutations, genome, region, meta):
+  SNVs = []
+  column_headings = [
+    'Chromosome'.lower(), 
+    'Start_Position'.lower(),
+    'End_Position'.lower(),
+    'Reference_Allele'.lower(), 
+    'Tumor_Seq_Allele1'.lower(), 
+    'Tumor_Seq_Allele2'.lower(), 
+    'Tumor_Sample_Barcode'.lower(),
+    'Variant_Type'.lower(), 
+    'ref_context' 
+  ]
+  column_heading_indices = fetch_column_heading_indices(meta['mutations'])
+  for row in mutations.fetch(region=region, parser=pysam.asTuple()):
+    mutation = {}
+    for column_heading in column_headings: 
+      try: 
+        mutation[column_heading] = row[column_heading_indices[column_heading]]
+      except KeyError: 
+        continue
+
+    if mutation['reference_allele'] == '-': continue # exclude INS
+    if len(mutation['reference_allele']) != 1: continue # exclude DEL, DNP, TNP, ONP
+    if mutation['tumor_seq_allele2'] not in {'A', 'T', 'G', 'C'}: continue # exclude DEL 
+
+    try: 
+      if mutation['reference_allele'] != mutation['tumor_seq_allele1']: # sanity check
+        print_json(mutation)
+        raise ValueError('Tumor allele 1 is not the same as reference allele') 
+      del mutation['tumor_seq_allele1']
+    except KeyError:
+      pass
+
+    start = int(mutation['start_position'])
+    mutation['position'] = start - 1
+    del mutation['start_position']
+
+    try: 
+      if start != int(mutation['end_position']): # sanity check for SNPs
+        print_json(mutation)
+        raise ValueError('SNPs must have equal start and end values') 
+      del mutation['end_position']
+    except KeyError:
+      pass
+
+    kmer = fetch_kmer_from_genome(genome, mutation['chromosome'], mutation['position'], meta['kmer_size'])
+    mutation['kmer'] = kmer
+    
+    if middle_base(kmer) != mutation['reference_allele'].upper(): # sanity check
+      print_json(mutation)
+      raise ValueError('Middle base of kmer does not match ref allele: {} {}'.format(
+        middle_base(kmer), 
+        mutation['reference_allele']
+      )) 
+    
+    try:
+      ref_context = mutation['ref_context'].upper() 
+      kmer_from_maf = fetch_kmer_from_sequence(ref_context, middle_index(ref_context), meta['kmer_size'])        
+      check_for_Ns(kmer_from_maf) # sanity check 
+      if kmer_from_maf != kmer: # sanity check
+        print_json(mutation)
+        raise ValueError('kmer from maf does not match kmer inferred from fasta') 
+      del mutation['ref_context']
+    except KeyError:
+      pass
+
+    try: 
+      if mutation['variant_type'] != 'SNP': # sanity check
+        print_json(mutation)
+        raise ValueError('variant_type is not SNP') 
+      del mutation['variant_type']
+    except KeyError:
+      pass
+
+    mutation['REF'] = mutation.pop('reference_allele')
+    mutation['ALT'] = mutation.pop('tumor_seq_allele2')
+
+    SNVs.append(mutation)
+  return SNVs
+

From 3e1e8ed30807755e2cd8c396c7cef8edbb177d42 Mon Sep 17 00:00:00 2001
From: Suchita Lulla <suchitalulla@gmail.com>
Date: Mon, 1 Nov 2021 18:43:40 -0600
Subject: [PATCH 4/9] takes .bed (no count or frequency data), added .html to
 .gitignore

---
 .gitignore                      |  2 +
 report/constraintview           |  2 -
 report/constraintview.py        | 34 ++++++++--------
 report/constraintview.yaml      |  4 +-
 report/create_constraint_txt.py | 17 +-------
 report/get_coords.py            | 29 +++++++------
 report/glyphs.py                | 72 +++++++++++++++++++--------------
 7 files changed, 80 insertions(+), 80 deletions(-)

diff --git a/.gitignore b/.gitignore
index dca87ef..475a9f5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,3 +27,5 @@ static
 node
 
 slurm-*.out
+
+.html
diff --git a/report/constraintview b/report/constraintview
index d4c10b9..5fce068 100755
--- a/report/constraintview
+++ b/report/constraintview
@@ -16,8 +16,6 @@ while [[ "$1" =~ ^- ]]; do
   shift
 done
 
-echo ${transcripts}
-
 cd ${CONSTRAINT_TOOLS}/report
 python create_constraint_txt.py constraintview.yaml
 python constraintview.py ${config_file} ${transcripts} -o ${output}
\ No newline at end of file
diff --git a/report/constraintview.py b/report/constraintview.py
index ddde395..536d4fe 100755
--- a/report/constraintview.py
+++ b/report/constraintview.py
@@ -25,7 +25,7 @@ def constraint_view_plot(plot_params, variant_params, user_line_params, transcri
     plot.toolbar.active_drag = None
     plot.yaxis[0].visible = False
     
-    ###VARIANTS###
+    ### VARIANTS ###
     if variant_ls:
         project_coords.map_point(variant_ls, transcript_dict['exons'])
         ray_glyph,circle_glyph,allele_counts,allele_frequencies = add_variant_glyph(plot_params, variant_params, plot, variant_ls)
@@ -36,31 +36,32 @@ def constraint_view_plot(plot_params, variant_params, user_line_params, transcri
             plot.add_tools(HoverTool(tooltips=tooltips_variations, renderers=[circle_glyph,ray_glyph], point_policy='follow_mouse', attachment='below'))
         glyph_dict['Variant'].extend([ray_glyph,circle_glyph])
         
-        axes['count'].append(add_variant_axis(plot_params, variant_params, plot, 'Allele count', allele_counts, visible=True))
-        axes['allele_frequency'].append(add_variant_axis(plot_params, variant_params, plot, 'Allele frequency',allele_frequencies, visible=False))
+        if variant_params['add_variant_axis']:
+            axes['count'].append(add_variant_axis(plot_params, variant_params, plot, 'Allele count', allele_counts, visible=True))
+            axes['allele_frequency'].append(add_variant_axis(plot_params, variant_params, plot, 'Allele frequency',allele_frequencies, visible=False))
 
     tooltips_features = [('Type','@feat_type'), ('Start (compact)', '@adj_start'), ('End (compact)', '@adj_end'), 
                       ('Start (chr)', '@true_start'), ('End (chr)', '@true_end'), ('Length', '@true_len')]
 
-    ###INTRONS###
+    ### INTRONS ###
     introns = project_coords.get_introns_from_exons(transcript_dict['exons'])
     introns_glyph = add_intron_glyph(plot_params, plot, introns)
     plot.add_tools(HoverTool(tooltips=tooltips_features, renderers=[introns_glyph], point_policy='follow_mouse', attachment='below'))    
     
-    ###EXONS###
+    ### EXONS ###
     exons_glyph,arrow_glyph = add_exon_glyph(plot_params, plot, transcript_dict['exons'], transcript_dict['direction'])
     plot.add_tools(HoverTool(tooltips=tooltips_features, renderers=[exons_glyph], point_policy='follow_mouse', attachment='below'))
     
     glyph_dict['Direction'].append(arrow_glyph)
     glyph_dict['exon'].append(exons_glyph)
 
-    ###UTRs###
+    ### UTRs ###
     project_coords.map_box(transcript_dict['UTRs'], transcript_dict['exons'])
     UTR_glyph = add_UTR_glyph(plot_params, plot, transcript_dict['UTRs'])
     plot.add_tools(HoverTool(tooltips=tooltips_features, renderers=[UTR_glyph], point_policy='follow_mouse', attachment='below'))    
     glyph_dict['UTRs'].append(UTR_glyph)
 
-    ###USER TRACKS###
+    ### USER TRACKS ###
     h = plot_params['track_height']
 
     for idx,track_name in enumerate(user_tracks):
@@ -79,7 +80,7 @@ def constraint_view_plot(plot_params, variant_params, user_line_params, transcri
         plot.add_layout(label)
         user_track_glyphs[track_name].append(label)
         
-    ###user lines###
+    ### USER LINES ###
     for idx,axis_name in enumerate(user_line_params):
         all_xs = []
         all_ys = []
@@ -106,7 +107,7 @@ def parse_args():
     parser.add_argument('-o', '--output', required=False, help='output filepath')
     args = parser.parse_args()
 
-    ###CONFIG###
+    ### CONFIG ###
     config_file = args.config_file
     print(config_file)
     # TODO what to do if config file doesn't have required params?
@@ -120,16 +121,16 @@ def parse_args():
         plot_params['transcript_height'] = 20 + len(user_track_params) * plot_params['track_height'] * 1.5
         plot_params['y0'] = plot_params['transcript_height'] + plot_params['exon_height'] / 2  # "0" for line plots
 
-    ###COLORS###
+    ### COLORS ###
     with open('named_colors.yaml') as f:
         named_colors = list(yaml.load_all(f, Loader=SafeLoader))[0]
 
-    ###GLYPH COLORS###
+    ### GLYPH COLORS ###
     for glyph_type in plot_params['glyph_colors']:
         color = plot_params['glyph_colors'][glyph_type]
         if color[0] != "#": plot_params['glyph_colors'][glyph_type] = named_colors[color]
 
-    ###TRACKS###
+    ### TRACKS ###
     for track_name in user_track_params:
         track_db = gff_to_db(user_track_params[track_name]['gtf_path'], user_track_params[track_name]['gtf_path'] + '.db')
         user_track_params[track_name]['db'] = track_db
@@ -138,13 +139,13 @@ def parse_args():
     track_colors = [named_colors[c] for c in palettes[plot_params['track_palette']]]
     plot_params['track_colors'] = track_colors
 
-    ###TRANSCRIPTS###
+    ### TRANSCRIPTS ###
     transcript_IDs = args.transcripts
     if transcript_IDs != 'all':
         transcript_IDs = transcript_IDs.strip('[').strip(']').split(',')
         transcript_IDs = [t.strip('\'') for t in transcript_IDs]
 
-    ###OUTPUT###
+    ### OUTPUT ###
     if args.output: output = args.output + '.html' if args.output[-5:] != '.html' else args.output
     else: output = 'plot.html'
     return plot_params,variant_params,user_track_params,user_line_params,transcript_IDs,output
@@ -156,7 +157,6 @@ def constraint_view():
     gff_db = gff_to_db(plot_params['gff_path'],plot_params['gff_path']+'test.db')
     
     gene_feature = get_gene_feature(gff_db, plot_params['gene_name'])
-    #print(gene_feature.start)
 
     if transcript_IDs == 'transcript_names':
         transcripts = get_transcript_dict(plot_params, gff_db, gene_feature, 'all')
@@ -166,7 +166,7 @@ def constraint_view():
     transcripts = get_transcript_dict(plot_params, gff_db, gene_feature, transcript_IDs)
     transcript_IDs = list(transcripts.keys()) #if 'all', transcript_IDs will become list of transcript names; if nonexistent IDs they are removed
     
-    variant_ls = get_variants(plot_params['variant_path']) if variant_params['plot_variants'] else []
+    variant_ls = get_variants(plot_params['variant_path'], gene_feature.start, gene_feature.end, variant_params['seqid']) if variant_params['plot_variants'] else []
     color_variants(plot_params, variant_params, variant_ls)
     user_tracks = {track_name: get_track(user_track_params, track_name) for track_name in user_track_params}
     for track_name in user_tracks: color_boxes(plot_params, user_track_params, track_name, user_tracks[track_name])
@@ -210,7 +210,7 @@ def constraint_view():
         else:
             sliders.append(None)
     
-    if variant_params['plot_variants']:
+    if variant_params['plot_variants'] and variant_params['add_variant_axis']:
         grid1 = [[checkbox, user_tracks_checkbox],[div_type, div_scale],[radio_group_type, radio_group_scale]] 
     else: grid1 = [[checkbox, user_tracks_checkbox]]
     
diff --git a/report/constraintview.yaml b/report/constraintview.yaml
index bc13d98..96fff90 100755
--- a/report/constraintview.yaml
+++ b/report/constraintview.yaml
@@ -6,7 +6,8 @@
 #variant_path: 'gnomad_v3_variants.bed'
 ###REMOTE PATHS
 gff_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/Homo_sapiens.GRCh38.104.gff3.db'
-variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomAD_v3.1.1_ENSG00000075043_2021_09_16_16_02_28.csv'
+#variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomAD_v3.1.1_ENSG00000075043_2021_09_16_16_02_28.csv'
+variant_path: /scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/gnomad/v3/gnomad_v3_variants.sorted.bed.gz
 #variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomad.exomes.r2.1.1.sites.20.vcf.bgz'
 model_path: '/scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/model.ptm.json' 
 ####Plot params
@@ -34,6 +35,7 @@ track_palette: 'blues' #palette to draw random track colors from; can be any one
 ---
 #variants
 plot_variants: True
+seqid: chr20
 min_lollipop_height: 15
 lollipop_radius: 5
 lollipop_line_width: 2
diff --git a/report/create_constraint_txt.py b/report/create_constraint_txt.py
index bd33998..95918f7 100644
--- a/report/create_constraint_txt.py
+++ b/report/create_constraint_txt.py
@@ -8,8 +8,6 @@
 from compute_mutation_counts import compute_mutation_counts
 from process_gene_gff import gff_to_db,get_gene_feature
 
-#def create_constraint_txt(gene_start, gene_end, chr_num, model, expected_out_filepath='expected_mut_counts.txt', observed_out_filepath='observed_mut_counts.txt', window_size=51, window_stride=25):
-
 def create_constraint_txt(gene_start, gene_end, chr_num, model, expected_out_filepath='expected_mut_counts.txt', observed_out_filepath='observed_mut_counts.txt', window_size=51, window_stride=25):
     exp_fi = open(expected_out_filepath, 'w')
     obs_fi = open(observed_out_filepath, 'w')
@@ -25,11 +23,6 @@ def create_constraint_txt(gene_start, gene_end, chr_num, model, expected_out_fil
     exp_fi.close()
     obs_fi.close()
 
-# parser = argparse.ArgumentParser(description='create_constraint_txt')
-# parser.add_argument('gff_path')
-# parser.add_argument('model_path')
-# parser.add_argument('gene_name')
-# parser.add_argument('seqid')
 parser = argparse.ArgumentParser(description='create_constraint_txt')
 parser.add_argument('config_file')
 args = parser.parse_args()
@@ -38,17 +31,9 @@ def create_constraint_txt(gene_start, gene_end, chr_num, model, expected_out_fil
     params = list(yaml.load_all(f, Loader=SafeLoader))
     plot_params = params[0]
 
-
 # 'test.db' to make sure .db does not get overwritten during development    
 #gff_db = gff_to_db(args.gff_path, args.gff_path + 'test.db')
 gff_db = gff_to_db(plot_params['gff_path'], plot_params['gff_path'] + 'test.db')
-#tmp = '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/Homo_sapiens.GRCh38.104.gff3.db'
 
 gene_feature = get_gene_feature(gff_db, plot_params['gene_name'])
-#gene_feature = get_gene_feature(gff_db, args.gene_name)
-
-#TODO maybe make this a config file
-#create_constraint_txt(gene_feature.start, gene_feature.end, args.seqid, args.model_path, expected_out_filepath='expected_mut_counts.txt', observed_out_filepath='observed_mut_counts.txt', window_size=51, window_stride=25)
-create_constraint_txt(gene_feature.start, gene_feature.end, plot_params['seqid'], plot_params['model_path'], expected_out_filepath='expected_mut_counts.txt', observed_out_filepath='observed_mut_counts.txt', window_size=51, window_stride=25)
-
-#python create_constraint_txt.py '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/Homo_sapiens.GRCh38.104.gff3.db' /scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/model.ptm.json KCNQ2 chr20
\ No newline at end of file
+create_constraint_txt(gene_feature.start, gene_feature.end, plot_params['seqid'], plot_params['model_path'], expected_out_filepath='expected_mut_counts.txt', observed_out_filepath='observed_mut_counts.txt', window_size=51, window_stride=25)
\ No newline at end of file
diff --git a/report/get_coords.py b/report/get_coords.py
index f52595e..7ecefac 100755
--- a/report/get_coords.py
+++ b/report/get_coords.py
@@ -12,13 +12,12 @@ def variant_type(annotation):
     #print('No classification for variant type {}; classified as "other"'.format(annotation))
     return 'MODIFIER'
 
-def get_variants(filepath):
-    
+def get_variants(filepath, start, end, seqid):
     def get_variants_vcf(vcf_path):
         variant_ls = []
         import tabix #putting import here for now because it doesn't work on local machine
         tb = tabix.open(vcf_path)
-        for idx,r in enumerate(tb.query('20',62037947,62137947)): #TODO don't hardcode params
+        for idx,r in enumerate(tb.query(seqid,start-1400000,end-1400000)): #TODO don't hardcode params
             variant_ls.append(dict(pos=int(r[1])+1400000, compact_pos=-1, ref=r[3], alt=r[4], #adding 1.4m bc this vcf is on old build
                               annotation=r[7].split(';')[-1].split('|')[1], severity=r[7].split(';')[-1].split('|')[2],
                               allele_count=int(r[7].split(';')[0].split('=')[1]),
@@ -40,15 +39,18 @@ def get_variants_csv(csv_path):
         return variant_ls
 
     def get_variants_bed(bed_path):
-        #variant_ls = []
-        #f = open(bed_path, 'r')
-        #with open(bed_path) as bedfile:
-            #print('a')
-            #print(bedfile.readlines()[:10])
-        #  #x = bedfile.readlines()
-
-
-        return []
+        import tabix #putting import here for now because it doesn't work on local machine
+        variant_ls = []
+        tb = tabix.open(bed_path)
+        #for idx,r in enumerate(tb.query('chr20',62037947,62137947)): #TODO don't hardcode params
+        #TODO cast seqid in parse_args
+        for idx,r in enumerate(tb.query(str(seqid),start-1400000,end-1400000)): #TODO don't hardcode params
+            variant_ls.append(dict(pos=int(r[1])+1400000, compact_pos=-1, ref=r[3], alt=r[4], #adding 1.4m bc this bed is on old build
+                             annotation=r[8], severity=variant_type(r[8]),
+                             allele_count=-1,
+                             allele_number=-1,
+                             allele_frequency=-1))
+        return variant_ls
     
     if filepath.split('.')[-2] == 'vcf':
         variant_ls = get_variants_vcf(filepath)
@@ -56,7 +58,8 @@ def get_variants_bed(bed_path):
     elif filepath.split('.')[-1] == 'csv':
         variant_ls = get_variants_csv(filepath)
 
-    elif filepath.split('.')[-1] == 'bed': #universal format
+    #TODO what to do about tabix'd vs non tabix'd?
+    elif '.bed' in filepath:
         variant_ls = get_variants_bed(filepath)
         
     else: raise ValueError('Invalid filepath: {}'.format(filepath))
diff --git a/report/glyphs.py b/report/glyphs.py
index c910a0d..8279e4e 100755
--- a/report/glyphs.py
+++ b/report/glyphs.py
@@ -2,9 +2,6 @@
 from bokeh.models import ColumnDataSource, Rect, Segment, Circle, MultiPolygons
 from colors import lighten_hex_color
 
-
-#param feature: (int, int); start and end of feature
-#return center: int; center point of feature
 def center_feature(feature):
     center = feature[0] + (feature[1] - feature[0])/2
     return center
@@ -18,7 +15,7 @@ def add_exon_glyph(plot_params, plot, exons, direction):
     w = [end - start for (start, end) in features_compact]
     h = [plot_params['exon_height'] - 4 for f in features_compact]
 
-    # METADATA
+    ### METADATA ###
     feat_type = ['Exon' for f in features_compact]
     adj_start = [start for (start, end) in features_compact]
     adj_end = [end for (start, end) in features_compact]
@@ -42,7 +39,7 @@ def add_exon_glyph(plot_params, plot, exons, direction):
         exon_glyph = plot.add_glyph(exon_source, exon_glyph, hover_glyph=hover_glyph)
         return exon_glyph, None
 
-    # ADD ARROWS#
+    ### ADD ARROWS ###
     def adjust_arrow_coords(coords, direction):
         ret = [j * (adj_end[i] - adj_start[i]) / 100 for j in coords]
         while (max(ret) - min(ret)) / plot_params['plot_width'] > 0.01:
@@ -92,14 +89,13 @@ def add_intron_glyph(plot_params, plot, introns, fill_alpha=1, width=14):
     w = [plot_params['intron_size'] * 2 for f in features_compact]  # avoid white spaces
     h = [plot_params['exon_height'] / 2 for f in features_compact]
 
-    ###METADATA
+    ### METADATA ###
     feat_type = ['Intron' for f in features_compact]
     adj_start = [start for (start, end) in features_compact]
     adj_end = [end for (start, end) in features_compact]
     true_start = [start for (start, end) in features_original]
     true_end = [end for (start, end) in features_original]
     true_len = [end - start + 1 for (start, end) in features_original]  # +1 for 1 indexed coords
-    ###
 
     source = ColumnDataSource(dict(x=x, y=y, w=w, h=h,
                                    feat_type=feat_type,
@@ -122,11 +118,11 @@ def add_UTR_glyph(plot_params, plot, UTRs, fill_alpha=0.4):
     features_compact = [(UTR['compact_start'], UTR['compact_end']) for UTR in UTRs]
     feat_type = [UTR['featuretype'] for UTR in UTRs]
     x = [center_feature(f) for f in features_compact]
-    y = [plot_params['transcript_height'] for f in features_compact]  # prev 10
+    y = [plot_params['transcript_height'] for f in features_compact]
     w = [end - start for (start, end) in features_compact]
     h = [plot_params['exon_height'] - 4 for f in features_compact]
 
-    # metadata
+    ### METADATA ###
     adj_start = [start for (start, end) in features_compact]
     adj_end = [end for (start, end) in features_compact]
     true_start = [start for (start, end) in features_original]
@@ -148,15 +144,19 @@ def add_UTR_glyph(plot_params, plot, UTRs, fill_alpha=0.4):
 
     return plot.add_glyph(source, glyph, hover_glyph=hover_glyph)
 
-
-def add_variant_glyph(plot_params, variant_params, plot, variant_ls, height=9, radius=5,
-                      line_width=2):  # height prev 18
+def add_variant_glyph(plot_params, variant_params, plot, variant_ls, line_width=2):
     variant_ls = [v for v in variant_ls if v['compact_pos'] >= 0]
     N = len(variant_ls)
     if N == 0: return None, None, 0, 0
     allele_counts = [v['allele_count'] for v in variant_ls]
     allele_numbers = [v['allele_number'] for v in variant_ls]
     allele_frequencies = [v['allele_frequency'] for v in variant_ls]
+
+    if sum(allele_frequencies) < 0: #TODO case where freq data but not cts
+        variant_params['add_variant_axis'] = False
+    else: variant_params['add_variant_axis'] = True
+    print(variant_params['add_variant_axis'])
+
     x = [v['compact_pos'] for v in variant_ls]
     y0s = [plot_params['y0'] - plot_params['exon_height'] / 2] * N
 
@@ -165,27 +165,24 @@ def get_y1(fn, ls):
         for idx, x in enumerate(ls_fn):
             if x < 0: raise ValueError('Lollipop height cannot be negative')
         y1_circle = [c * (plot_params['plot_height'] - plot_params['y0'] - variant_params[
-            'min_lollipop_height'] - radius - line_width - 2) / max([c for c in ls_fn]) + plot_params['y0'] +
+            'min_lollipop_height'] - variant_params['lollipop_radius'] - line_width - 2) / max([c for c in ls_fn]) + plot_params['y0'] +
                      variant_params['min_lollipop_height'] for c in ls_fn]
-        y1_segment = [y - radius for y in y1_circle]
+        y1_segment = [y - variant_params['lollipop_radius'] for y in y1_circle]
         return y1_circle, y1_segment
 
-    y1_ci_li_ct, y1_sg_li_ct = get_y1(lambda x: x, allele_counts)
-    y1_ci_lg_ct, y1_sg_lg_ct = get_y1(lambda x: np.log10(x) if x > 0 else 0, allele_counts)
-    y1_ci_li_fr, y1_sg_li_fr = get_y1(lambda x: x, allele_frequencies)
-    y1_ci_lg_fr, y1_sg_lg_fr = get_y1(lambda x: -np.log10(x) if x > 0 else 0, allele_frequencies)
-    r = [radius] * N
-    info = ['info'] * N
-
+    r = [variant_params['lollipop_radius']] * N
     colors = [v['color'] for v in variant_ls]
 
     hover_colors = [lighten_hex_color(c, 40) for c in colors]
 
-    source = ColumnDataSource(dict(x=x, r=r, y0=y0s, y1_circle=y1_ci_li_ct, y1_segment=y1_sg_li_ct,
-                                   y1_ci_li_ct=y1_ci_li_ct, y1_sg_li_ct=y1_sg_li_ct,
-                                   y1_ci_lg_ct=y1_ci_lg_ct, y1_sg_lg_ct=y1_sg_lg_ct,
-                                   y1_ci_li_fr=y1_ci_li_fr, y1_sg_li_fr=y1_sg_li_fr,
-                                   y1_ci_lg_fr=y1_ci_lg_fr, y1_sg_lg_fr=y1_sg_lg_fr,
+    if variant_params['add_variant_axis']:
+        y1_circle,y1_segment = get_y1(lambda x: x, allele_counts)
+    else:
+        y1_circle,y1_segment = get_y1(lambda x: x/2, [1 for v in variant_ls])
+        y1_circle = [y1/2 for y1 in y1_circle] #if lollipop heights don't hold meaning, set them to 1/2 max height
+        y1_segment = [y1/2 for y1 in y1_segment]
+
+    cds_dict = dict(x=x, r=r, y0=y0s, y1_circle=y1_circle, y1_segment=y1_segment, 
                                    allele_counts=allele_counts,
                                    allele_numbers=allele_numbers,
                                    allele_frequencies=allele_frequencies,
@@ -194,7 +191,22 @@ def get_y1(fn, ls):
                                    alt=[v['alt'] for v in variant_ls],
                                    ann=[v['annotation'] for v in variant_ls],
                                    sev=[v['severity'] for v in variant_ls],
-                                   colors=colors, hover_colors=hover_colors, line_alpha=[1 for v in variant_ls]))
+                                   colors=colors, hover_colors=hover_colors, line_alpha=[1 for v in variant_ls])
+
+    if variant_params['add_variant_axis']:
+        y1_ci_li_ct, y1_sg_li_ct = get_y1(lambda x: x, allele_counts)
+        y1_ci_lg_ct, y1_sg_lg_ct = get_y1(lambda x: np.log10(x) if x > 0 else 0, allele_counts)
+        y1_ci_li_fr, y1_sg_li_fr = get_y1(lambda x: x, allele_frequencies)
+        y1_ci_lg_fr, y1_sg_lg_fr = get_y1(lambda x: -np.log10(x) if x > 0 else 0, allele_frequencies)
+
+        variant_axis_dict = dict(
+            y1_ci_li_ct=y1_ci_li_ct, y1_sg_li_ct=y1_sg_li_ct,
+            y1_ci_lg_ct=y1_ci_lg_ct, y1_sg_lg_ct=y1_sg_lg_ct,
+            y1_ci_li_fr=y1_ci_li_fr, y1_sg_li_fr=y1_sg_li_fr,
+            y1_ci_lg_fr=y1_ci_lg_fr, y1_sg_lg_fr=y1_sg_lg_fr)
+        cds_dict.update(variant_axis_dict)
+
+    source = ColumnDataSource(cds_dict)
 
     segment_glyph = plot.segment(source=source, x0='x', y0='y0', x1='x', y1='y1_segment', line_color='colors',
                                  line_width=line_width, line_alpha='line_alpha')
@@ -224,7 +236,7 @@ def add_track_glyph(plot, tracks, height, y_pos):
     h = [height for f in tracks_compact]
     hover_colors = [lighten_hex_color(color, 40) for color in colors]
 
-    # metadata
+    ### METADATA ###
     adj_start = [start for (start, end) in tracks_compact]
     adj_end = [end for (start, end) in tracks_compact]
     true_start = [start for (start, end) in tracks_original]
@@ -276,6 +288,4 @@ def smooth_ls(ls, k=1):
                                            line_alpha='line_alpha')
 
     multi_line_glyph.nonselection_glyph = None
-    return multi_line_glyph
-
-
+    return multi_line_glyph
\ No newline at end of file

From e92794e03e75e74073a59c07f6c8b1513eb3cde5 Mon Sep 17 00:00:00 2001
From: Suchita Lulla <suchitalulla@gmail.com>
Date: Tue, 9 Nov 2021 18:49:27 -0700
Subject: [PATCH 5/9] Changes to fetch_SNVs

---
 predict-constraint/compute_mutation_counts.py |   7 +-
 report/constraintview.yaml                    |   3 +-
 report/get_coords.py                          |  10 +-
 report/plot.html                              |  10 +-
 report/project_coords.py                      |   1 -
 tests/compute-mutation-counts.sh              |   2 +-
 utilities/fetch_SNVs_new.py                   | 120 ------------------
 7 files changed, 19 insertions(+), 134 deletions(-)
 delete mode 100644 utilities/fetch_SNVs_new.py

diff --git a/predict-constraint/compute_mutation_counts.py b/predict-constraint/compute_mutation_counts.py
index 93b496d..1bece36 100644
--- a/predict-constraint/compute_mutation_counts.py
+++ b/predict-constraint/compute_mutation_counts.py
@@ -119,8 +119,10 @@ def compute_SNV_positions_frequencies(SNVs, filter_function):
   SNV_positions = [SNV['position'] for SNV in SNVs if filter_function(SNV['kmer'])]  
   # find frequency of each unique coordinate using Counter: 
   # https://stackoverflow.com/a/2162045/6674256  
-  SNV_positions_frequencies = collections.Counter(SNV_positions)
-  return tuple(zip(*SNV_positions_frequencies.items()))
+  #SNV_positions_frequencies = collections.Counter(SNV_positions)
+  SNV_positions_frequencies = [SNV['ac'] for SNV in SNVs if filter_function(SNV['kmer'])]
+  #return tuple(zip(*SNV_positions_frequencies.items()))
+  return (SNV_positions, SNV_positions_frequencies)
 
 def compute_lollipops(mutations, genome, region, model):
   SNVs = fetch_SNVs(mutations, genome, region, meta=model)
@@ -175,6 +177,7 @@ def parse_arguments():
 
 if __name__ == '__main__':
   args = parse_arguments() 
+
   
   print(
     json.dumps(
diff --git a/report/constraintview.yaml b/report/constraintview.yaml
index 96fff90..02212ab 100755
--- a/report/constraintview.yaml
+++ b/report/constraintview.yaml
@@ -35,7 +35,8 @@ track_palette: 'blues' #palette to draw random track colors from; can be any one
 ---
 #variants
 plot_variants: True
-seqid: chr20
+#seqid: 20 #for .vcf
+seqid: chr20 #for .bed
 min_lollipop_height: 15
 lollipop_radius: 5
 lollipop_line_width: 2
diff --git a/report/get_coords.py b/report/get_coords.py
index 7ecefac..f358f3a 100755
--- a/report/get_coords.py
+++ b/report/get_coords.py
@@ -17,7 +17,8 @@ def get_variants_vcf(vcf_path):
         variant_ls = []
         import tabix #putting import here for now because it doesn't work on local machine
         tb = tabix.open(vcf_path)
-        for idx,r in enumerate(tb.query(seqid,start-1400000,end-1400000)): #TODO don't hardcode params
+        #TODO cast seqid in parse_args
+        for idx,r in enumerate(tb.query(str(seqid),start-1400000,end-1400000)):
             variant_ls.append(dict(pos=int(r[1])+1400000, compact_pos=-1, ref=r[3], alt=r[4], #adding 1.4m bc this vcf is on old build
                               annotation=r[7].split(';')[-1].split('|')[1], severity=r[7].split(';')[-1].split('|')[2],
                               allele_count=int(r[7].split(';')[0].split('=')[1]),
@@ -42,9 +43,10 @@ def get_variants_bed(bed_path):
         import tabix #putting import here for now because it doesn't work on local machine
         variant_ls = []
         tb = tabix.open(bed_path)
-        #for idx,r in enumerate(tb.query('chr20',62037947,62137947)): #TODO don't hardcode params
         #TODO cast seqid in parse_args
-        for idx,r in enumerate(tb.query(str(seqid),start-1400000,end-1400000)): #TODO don't hardcode params
+        #for idx,r in enumerate(tb.query(str(seqid),start-1400000,end-1400000)):
+        for idx,r in enumerate(tb.query(str(seqid),start,end)):
+            if idx<10: print(r)
             variant_ls.append(dict(pos=int(r[1])+1400000, compact_pos=-1, ref=r[3], alt=r[4], #adding 1.4m bc this bed is on old build
                              annotation=r[8], severity=variant_type(r[8]),
                              allele_count=-1,
@@ -92,7 +94,7 @@ def get_track(user_track_params, track_name, strand='-'):
     boxes = []
     db = user_track_params[track_name]['db']
     seqid = user_track_params[track_name]['seqid']
-    for s in list(db.region(seqid=seqid, featuretype='exon', strand=strand)):  # [::-1]:
+    for s in list(db.region(seqid=seqid, featuretype='exon', strand=strand)):
         box_dict = dict(ID=s['gene_id'][0], start=s.start, end=s.end, compact_start=-1,
                         compact_end=-1)  # more than one gene name?
         boxes.append(box_dict)
diff --git a/report/plot.html b/report/plot.html
index 311168f..54caa98 100644
--- a/report/plot.html
+++ b/report/plot.html
@@ -35,14 +35,14 @@
           
           
             
-              <div class="bk-root" id="45ea8eef-9080-4f94-ad31-06a404db5be1" data-root-id="1444"></div>
+              <div class="bk-root" id="6868313e-3b1f-474a-b925-5c6fe3935f1d" data-root-id="6537"></div>
             
           
         
       
       
-        <script type="application/json" id="2012">
-          {"3214713b-8250-4154-a123-b5eebf11f792":{"defs":[],"roots":{"references":[{"attributes":{"formatter":{"id":"1432"},"major_label_policy":{"id":"1433"},"ticker":{"id":"1154"},"visible":false},"id":"1153","type":"LinearAxis"},{"attributes":{"args":{"axes":{"Coverage":[],"Mutation counts":[],"allele_frequency":[{"id":"1052"}],"count":[{"id":"1048"}]},"axis_names":["Allele count","Allele frequency"],"ori_y_coords":[40.0,25.0,10.0],"plot_ls":[{"id":"1004"}],"plot_params":{"exon_height":16,"gene_name":"KCNQ2","gff_path":"/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/Homo_sapiens.GRCh38.104.gff3.db","glyph_colors":{"UTR":"#969696","arrow":"#252525","exon":"#525252","intron":"#bdbdbd","variant":"#2f4858"},"intron_size":20,"model_path":"/scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/model.ptm.json","plot_UTRs":true,"plot_direction":true,"plot_height":200,"plot_width":1500,"seqid":"chr20","track_colors":["#43aa8b","#577590","#7161ef","#404e7c","#613dc1","#0d3b66","#a1b5d8","#031d44","#86bbd8","#2f4858"],"track_height":10,"track_palette":"blues","transcript_height":65.0,"variant_path":"/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomAD_v3.1.1_ENSG00000075043_2021_09_16_16_02_28.csv","y0":73.0},"s0_arrow":[{"id":"1065"}],"user_track_glyphs":{"domains":[{"id":"1086"},{"id":"1092"}],"domains2":[{"id":"1098"},{"id":"1104"}],"domains3":[{"id":"1110"},{"id":"1116"}]},"user_track_names":["domains","domains2","domains3"]},"code":"\n        const transcript_h = plot_params['transcript_height']\n        const exon_h = plot_params['exon_height']\n        const track_h = plot_params['track_height']\n            \n        function setVis(glyphs, vis){\n            for (let i = 0; i &lt; glyphs.length; i++){\n                if(glyphs[i] != null){\n                    glyphs[i].visible = vis\n                }\n            }\n        }\n        \n        function setAxesStart(start){\n            for (let i = 0; i &lt; axis_names.length; i++){\n                for (let j = 0; j &lt; plot_ls.length; j++){\n                    plot_ls[j].y_range.start = start\n                    plot_ls[j].extra_y_ranges[axis_names[i]].start = start\n                }\n            }\n        }\n        \n        //in LabelSet source is called source whereas in GlyphRenderer source is called data_source for no apparent reason\n        function get_source(glyph){\n            try {glyph.data_source.data; return glyph.data_source}\n            catch (err) {return glyph.source}\n        }\n        \n        function setY(track_name,y){\n            console.log(y)\n            for (let i = 0; i &lt; user_track_glyphs[track_name].length; i++){\n                for (let j = 0; j &lt; get_source(user_track_glyphs[track_name][i]).data['y'].length; j++){\n                    if (i%2==0) {get_source(user_track_glyphs[track_name][i]).data['y'][j] = y}\n                    else {get_source(user_track_glyphs[track_name][i]).data['y'][j] = y-track_h}    \n                }\n                console.log(user_track_glyphs[track_name][i])\n                get_source(user_track_glyphs[track_name][i]).change.emit()\n            }\n        }\n        \n        function adjust_arrow(s0_arrow,start){ \n            \n            for (let i = 0; i &lt; s0_arrow.length; i++){\n                for (let j = 0; j &lt; s0_arrow[i].data['y'].length/2; j++){\n                    //triangle\n                    s0_arrow[i].data['y'][j*2+1][0][0][0] = transcript_h-exon_h/2 + start/(track_h*1.5) //start 57\n                    s0_arrow[i].data['y'][j*2+1][0][0][1] = transcript_h+exon_h/2 - start/(track_h*1.5)\n                    //rectangle\n                    s0_arrow[i].data['y'][j*2][0][0][0] = transcript_h-exon_h/5 + start/(track_h*1.5*3)\n                    s0_arrow[i].data['y'][j*2][0][0][1] = transcript_h+exon_h/5 - start/(track_h*1.5*3)\n                    s0_arrow[i].data['y'][j*2][0][0][2] = transcript_h+exon_h/5 - start/(track_h*1.5*3)\n                    s0_arrow[i].data['y'][j*2][0][0][3] = transcript_h-exon_h/5 + start/(track_h*1.5*3)\n                }\n                s0_arrow[i].change.emit()\n            }\n        }\n        \n        var temp = 0\n        var y_co = 0\n        \n        for (let i = 0; i &lt; user_track_names.length; i++){\n            if (cb_obj.active.includes(i)) {\n                setVis(user_track_glyphs[user_track_names[i]],true)\n                setY(user_track_names[i], ori_y_coords[temp])\n                y_co = ori_y_coords[temp]\n                temp++\n            }\n            else {setVis(user_track_glyphs[user_track_names[i]],false)}\n        }\n        var start = 0\n        if (y_co==0){start = plot_params['transcript_height']-plot_params['exon_height']/2}\n        else {start = y_co-ori_y_coords[ori_y_coords.length-1]}\n        setAxesStart(start)\n        adjust_arrow(s0_arrow,start)\n    "},"id":"1201","type":"CustomJS"},{"attributes":{"args":{"fill_area_ls":[false,false],"glyph_ls":[{"id":"1132"},{"id":"1138"}]},"code":"\n        function smooth(y,k,fill_area) {\n            //console.log(fill_area)\n            var smoothed_ls = [ ... y]\n            if (smoothed_ls.length &lt;= 2) {return smoothed_ls}\n            if (fill_area) {smoothed_ls = smoothed_ls.slice(1,smoothed_ls.length-1)}\n            \n            for (let i = 0; i &lt; smoothed_ls.length; i += k){\n                const window_avg = mean(smoothed_ls.slice(i, i+k))\n                for (let j = i; j &lt; i + k; j++){\n                    if (j &lt; smoothed_ls.length-1) { smoothed_ls[j] = window_avg }\n                }\n            }\n            if (fill_area) {return [y[0], ...smoothed_ls, y[y.length-1]]}\n            \n            else {return smoothed_ls}\n        }\n        \n        function mean(y) { return y.reduce((i, j) =&gt; i + j) / y.length }\n        \n        console.log(glyph_ls)\n        for (let i = 0; i &lt; glyph_ls.length; i++){\n            //console.log(fill_area_ls[i])\n            for (let j = 0; j &lt; glyph_ls[i].data_source.data['y'].length; j++){\n                glyph_ls[i].data_source.data['y'][j] = smooth(glyph_ls[i].data_source.data['y_unsmoothed'][j], cb_obj.value, fill_area_ls[i])\n            }\n            glyph_ls[i].data_source.change.emit()\n        }\n        \n    "},"id":"1214","type":"CustomJS"},{"attributes":{},"id":"1261","type":"UnionRenderers"},{"attributes":{},"id":"1262","type":"Selection"},{"attributes":{"args":{"axes":{"Coverage":[],"Mutation counts":[],"allele_frequency":[{"id":"1052"}],"count":[{"id":"1048"}]},"mlo_lg_ct":[{"114.25":"4.35","140.5":"4.66","166.75":"4.83","193":"4.96","88":"0.00"}],"mlo_lg_fr":[{"114.25":"0.82","140.5":"0.52","166.75":"0.35","193":"0.22","88":"0.00"}],"mlo_li_ct":[{"114.25":"22630.00","140.5":"45259.00","166.75":"67888.00","193":"90517.00","88":"1.00"}],"mlo_li_fr":[{"114.25":"0.15","140.5":"0.30","166.75":"0.45","193":"0.60","88":"0.00"}],"radio_group_scale":{"id":"1209"},"variant":[{"id":"1036"},{"id":"1042"}]},"code":"        \n        function setAxis(label, mlo){\n            for (let i = 0; i &lt; axes['count'].length; i++){\n                axes['count'][i].axis_label = label\n                axes['count'][i].major_label_overrides = mlo[i]\n            }   \n        }\n        \n        for (let 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         </script>
         <script type="text/javascript">
           (function() {
@@ -51,8 +51,8 @@
                 (function(root) {
                   function embed_document(root) {
                     
-                  var docs_json = document.getElementById('2012').textContent;
-                  var render_items = [{"docid":"3214713b-8250-4154-a123-b5eebf11f792","root_ids":["1444"],"roots":{"1444":"45ea8eef-9080-4f94-ad31-06a404db5be1"}}];
+                  var docs_json = document.getElementById('13369').textContent;
+                  var render_items = [{"docid":"7f99df71-5338-4bf5-864a-058b56fb4787","root_ids":["6537"],"roots":{"6537":"6868313e-3b1f-474a-b925-5c6fe3935f1d"}}];
                   root.Bokeh.embed.embed_items(docs_json, render_items);
                 
                   }
diff --git a/report/project_coords.py b/report/project_coords.py
index 32a23ee..a6acab0 100755
--- a/report/project_coords.py
+++ b/report/project_coords.py
@@ -462,7 +462,6 @@ def map_point(point_coords, exons):
                 coord['compact_pos'] = exon['compact_start'] + coord['pos'] - exon['start']
                 break
 
-
 def get_introns_from_exons(exons):
     introns = []
 
diff --git a/tests/compute-mutation-counts.sh b/tests/compute-mutation-counts.sh
index 88f691c..ca402eb 100644
--- a/tests/compute-mutation-counts.sh
+++ b/tests/compute-mutation-counts.sh
@@ -15,7 +15,7 @@ export PYTHONPATH="${CONSTRAINT_TOOLS}/utilities:${CONSTRAINT_TOOLS}/predict-con
 PATH="${CONSTRAINT_TOOLS}/bin:$PATH" 
 
 model="/scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/model.ptm.json" 
-region="chr1:100,000-100,200"
+region="chr1:100,000-100,600"
 window_size="51" 
 window_stride="25"
 
diff --git a/utilities/fetch_SNVs_new.py b/utilities/fetch_SNVs_new.py
deleted file mode 100644
index ac523b6..0000000
--- a/utilities/fetch_SNVs_new.py
+++ /dev/null
@@ -1,120 +0,0 @@
-# pysam API: 
-# https://github.com/pysam-developers/pysam/blob/b82cbcae22c088e64fdb58f8acaf1e9773c7b088/pysam/libctabix.pyx
-import pysam
-
-from column_headings import fetch_column_heading_indices
-from colorize import print_json
-from kmer import fetch_kmer_from_genome, fetch_kmer_from_sequence, middle_base, middle_index, check_for_Ns
-
-def fetch_SNVs(mutations, genome, region, meta):
-  #mutations = "/scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/gnomad/v3/gnomad_v3_variants.sorted.bed.gz "
-  #mutations = "/scratch/ucgd/lustre-work/quinlan/u6018199/constraint-tools/data/icgc/mutations.sorted.maf.gz"
-  #print(mutations)
-  SNVs = []
-  column_headings = [
-    #'Chromosome'.lower(), 
-    #'Start_Position'.lower(),
-    #'End_Position'.lower(),
-    #'Reference_Allele'.lower(), 
-    #'Tumor_Seq_Allele1'.lower(), 
-    #'Tumor_Seq_Allele2'.lower(), 
-    #'Tumor_Sample_Barcode'.lower(),
-    #'Variant_Type'.lower(), 
-    #'ref_context' 
-    'chrom', 'start', 'end', 'ref', 'alt', 'allele_count', 'variant_type'
-  ]
-  column_heading_indices = fetch_column_heading_indices(meta['mutations'])
-<<<<<<< HEAD
-  #print('a')
-=======
->>>>>>> 4a84ea0234929fcd60e054e7ad01ba488fe2677b
-  #print('column_heading_indices',column_heading_indices)
-  for row in mutations.fetch(region=region, parser=pysam.asTuple()):
-    mutation = {}
-    for column_heading in column_headings: 
-      try: 
-        mutation[column_heading] = row[column_heading_indices[column_heading]]
-      except KeyError: 
-        continue
-    #if mutation['reference_allele'] == '-': continue # exclude INS
-    #print(mutation['start'])
-    if mutation['ref'] == '-': continue # exclude INS
-    #if len(mutation['reference_allele']) != 1: continue # exclude DEL, DNP, TNP, ONP
-    if len(mutation['ref']) != 1: continue
-    #if mutation['tumor_seq_allele2'] not in {'A', 'T', 'G', 'C'}: continue # exclude DEL
-    if mutation['alt'] not in {'A', 'T', 'G', 'C'}: continue
-    
-<<<<<<< HEAD
-    ###I don't think we need this block???
-=======
-    ###I don't think we need this block for this file format?
->>>>>>> 4a84ea0234929fcd60e054e7ad01ba488fe2677b
-    #try: 
-      #if mutation['reference_allele'] != mutation['tumor_seq_allele1']: # sanity check
-    #    print_json(mutation)
-    #    raise ValueError('Tumor allele 1 is not the same as reference allele') 
-    #  del mutation['tumor_seq_allele1']
-    #except KeyError:
-    #  pass
-
-    #start = int(mutation['start_position'])
-    start = int(mutation['start'])
-    #mutation['position'] = start - 1
-    mutation['position'] = start
-    #del mutation['start_position']
-    del mutation['start']
-
-    try: 
-      #if start != int(mutation['end_position']): # sanity check for SNPs
-      if start != int(mutation['end'])-1: # sanity check for SNPs
-        print_json(mutation)
-        #raise ValueError('SNPs must have equal start and end values') 
-        raise ValueError('SNPs must start and end values 1 bp apart') 
-      #del mutation['end_position']
-      del mutation['end']
-    except KeyError:
-      pass
-
-    #kmer = fetch_kmer_from_genome(genome, mutation['chromosome'], mutation['position'], meta['kmer_size'])
-    kmer = fetch_kmer_from_genome(genome, mutation['chrom'], mutation['position'], meta['kmer_size'])
-    mutation['kmer'] = kmer
-    
-    #if middle_base(kmer) != mutation['reference_allele'].upper(): # sanity check
-    if middle_base(kmer) != mutation['ref'].upper(): # sanity check
-      print_json(mutation)
-      raise ValueError('Middle base of kmer does not match ref allele: {} {} {}'.format(
-        middle_base(kmer), 
-        kmer,
-        #mutation['reference_allele']
-        mutation['ref']
-      )) 
-    
-    try:
-      ref_context = mutation['ref_context'].upper() 
-      kmer_from_maf = fetch_kmer_from_sequence(ref_context, middle_index(ref_context), meta['kmer_size'])        
-      check_for_Ns(kmer_from_maf) # sanity check 
-      if kmer_from_maf != kmer: # sanity check
-        print_json(mutation)
-        raise ValueError('kmer from maf does not match kmer inferred from fasta') 
-      del mutation['ref_context']
-    except KeyError:
-      pass
-
-    try: 
-      #if mutation['variant_type'] != 'SNP': # sanity check
-      if mutation['feature_type'] != 'SNP': # sanity check
-        print_json(mutation)
-        raise ValueError('variant_type is not SNP') 
-      #del mutation['variant_type']
-      del mutation['feature_type']
-    except KeyError:
-      pass
-
-    #mutation['REF'] = mutation.pop('reference_allele')
-    mutation['REF'] = mutation.pop('ref')
-    #mutation['ALT'] = mutation.pop('tumor_seq_allele2')
-    mutation['ALT'] = mutation.pop('alt')
-
-    SNVs.append(mutation)
-  return SNVs
-

From e1b72d503d044f7c2ea96245eddc9e9fac1686a9 Mon Sep 17 00:00:00 2001
From: Suchita Lulla <suchitalulla@gmail.com>
Date: Tue, 9 Nov 2021 19:18:17 -0700
Subject: [PATCH 6/9] fixed 0 variants bug

---
 report/constraintview.yaml  |  8 ++--
 report/get_coords.py        |  2 +-
 report/glyphs.py            |  3 +-
 report/plot.html            | 10 ++---
 utilities/fetch_SNVs_old.py | 89 -------------------------------------
 5 files changed, 11 insertions(+), 101 deletions(-)
 delete mode 100644 utilities/fetch_SNVs_old.py

diff --git a/report/constraintview.yaml b/report/constraintview.yaml
index 02212ab..c4731f3 100755
--- a/report/constraintview.yaml
+++ b/report/constraintview.yaml
@@ -7,8 +7,8 @@
 ###REMOTE PATHS
 gff_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/Homo_sapiens.GRCh38.104.gff3.db'
 #variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomAD_v3.1.1_ENSG00000075043_2021_09_16_16_02_28.csv'
-variant_path: /scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/gnomad/v3/gnomad_v3_variants.sorted.bed.gz
-#variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomad.exomes.r2.1.1.sites.20.vcf.bgz'
+#variant_path: /scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/gnomad/v3/gnomad_v3_variants.sorted.bed.gz
+variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomad.exomes.r2.1.1.sites.20.vcf.bgz'
 model_path: '/scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/model.ptm.json' 
 ####Plot params
 gene_name: 'KCNQ2'
@@ -35,8 +35,8 @@ track_palette: 'blues' #palette to draw random track colors from; can be any one
 ---
 #variants
 plot_variants: True
-#seqid: 20 #for .vcf
-seqid: chr20 #for .bed
+seqid: 20 #for .vcf
+#seqid: chr20 #for .bed
 min_lollipop_height: 15
 lollipop_radius: 5
 lollipop_line_width: 2
diff --git a/report/get_coords.py b/report/get_coords.py
index f358f3a..57d8ac0 100755
--- a/report/get_coords.py
+++ b/report/get_coords.py
@@ -46,7 +46,7 @@ def get_variants_bed(bed_path):
         #TODO cast seqid in parse_args
         #for idx,r in enumerate(tb.query(str(seqid),start-1400000,end-1400000)):
         for idx,r in enumerate(tb.query(str(seqid),start,end)):
-            if idx<10: print(r)
+            #if idx<10: print(r)
             variant_ls.append(dict(pos=int(r[1])+1400000, compact_pos=-1, ref=r[3], alt=r[4], #adding 1.4m bc this bed is on old build
                              annotation=r[8], severity=variant_type(r[8]),
                              allele_count=-1,
diff --git a/report/glyphs.py b/report/glyphs.py
index 8279e4e..bd7f1c7 100755
--- a/report/glyphs.py
+++ b/report/glyphs.py
@@ -147,7 +147,7 @@ def add_UTR_glyph(plot_params, plot, UTRs, fill_alpha=0.4):
 def add_variant_glyph(plot_params, variant_params, plot, variant_ls, line_width=2):
     variant_ls = [v for v in variant_ls if v['compact_pos'] >= 0]
     N = len(variant_ls)
-    if N == 0: return None, None, 0, 0
+    if N == 0: return None, None, [0], [0]
     allele_counts = [v['allele_count'] for v in variant_ls]
     allele_numbers = [v['allele_number'] for v in variant_ls]
     allele_frequencies = [v['allele_frequency'] for v in variant_ls]
@@ -155,7 +155,6 @@ def add_variant_glyph(plot_params, variant_params, plot, variant_ls, line_width=
     if sum(allele_frequencies) < 0: #TODO case where freq data but not cts
         variant_params['add_variant_axis'] = False
     else: variant_params['add_variant_axis'] = True
-    print(variant_params['add_variant_axis'])
 
     x = [v['compact_pos'] for v in variant_ls]
     y0s = [plot_params['y0'] - plot_params['exon_height'] / 2] * N
diff --git a/report/plot.html b/report/plot.html
index 54caa98..f93bc43 100644
--- a/report/plot.html
+++ b/report/plot.html
@@ -35,14 +35,14 @@
           
           
             
-              <div class="bk-root" id="6868313e-3b1f-474a-b925-5c6fe3935f1d" data-root-id="6537"></div>
+              <div class="bk-root" id="7d07f30c-7e1f-4e28-8438-eb6dc4d30951" data-root-id="7095"></div>
             
           
         
       
       
-        <script type="application/json" id="13369">
-          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s1_arrow){\n            const N_arrow = s1_arrow.data['x'].length\n            for (let i = 0; i &lt; N_arrow; i++){\n                s0_arrow.data['x'][i][0][0] = s1_arrow.data['x'][i][0][0]\n            }\n        }\n        \n        function adjust_x_axis() {\n            plot.x_range.start = active_exon_start\n            plot.x_range.end = active_exon_end\n        }\n        \n        function reset_x_axis() {\n            plot.x_range.start = 0\n            plot.x_range.end = s1_exon.data['adj_end'][N_exon-1]\n        }\n                       \n        if(cb_obj.active){\n            adjust_x_axis()\n            if (s1_arrow != null) {adjust_arrow(s0_arrow, s1_arrow)}\n        } else{\n            reset_x_axis()\n            if (s1_arrow != null) {reset_arrow(s0_arrow, s1_arrow)}\n        }\n        if (s1_arrow != null) {s0_arrow.change.emit()}\n    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s1_arrow){\n            const N_arrow = s1_arrow.data['x'].length\n            for (let i = 0; i &lt; N_arrow; i++){\n                s0_arrow.data['x'][i][0][0] = s1_arrow.data['x'][i][0][0]\n            }\n        }\n        \n        function adjust_x_axis() {\n            plot.x_range.start = active_exon_start\n            plot.x_range.end = active_exon_end\n        }\n        \n        function reset_x_axis() {\n            plot.x_range.start = 0\n            plot.x_range.end = s1_exon.data['adj_end'][N_exon-1]\n        }\n                       \n        if(cb_obj.active){\n            adjust_x_axis()\n            if (s1_arrow != null) {adjust_arrow(s0_arrow, s1_arrow)}\n        } else{\n            reset_x_axis()\n            if (s1_arrow != null) {reset_arrow(s0_arrow, s1_arrow)}\n        }\n        if (s1_arrow != null) {s0_arrow.change.emit()}\n    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         </script>
         <script type="text/javascript">
           (function() {
@@ -51,8 +51,8 @@
                 (function(root) {
                   function embed_document(root) {
                     
-                  var docs_json = document.getElementById('13369').textContent;
-                  var render_items = [{"docid":"7f99df71-5338-4bf5-864a-058b56fb4787","root_ids":["6537"],"roots":{"6537":"6868313e-3b1f-474a-b925-5c6fe3935f1d"}}];
+                  var docs_json = document.getElementById('14503').textContent;
+                  var render_items = [{"docid":"859509d1-fb08-4a9a-92fb-32c05e8f7362","root_ids":["7095"],"roots":{"7095":"7d07f30c-7e1f-4e28-8438-eb6dc4d30951"}}];
                   root.Bokeh.embed.embed_items(docs_json, render_items);
                 
                   }
diff --git a/utilities/fetch_SNVs_old.py b/utilities/fetch_SNVs_old.py
deleted file mode 100644
index a01d467..0000000
--- a/utilities/fetch_SNVs_old.py
+++ /dev/null
@@ -1,89 +0,0 @@
-# pysam API: 
-# https://github.com/pysam-developers/pysam/blob/b82cbcae22c088e64fdb58f8acaf1e9773c7b088/pysam/libctabix.pyx
-import pysam
-
-from column_headings import fetch_column_heading_indices
-from colorize import print_json
-from kmer import fetch_kmer_from_genome, fetch_kmer_from_sequence, middle_base, middle_index, check_for_Ns
-
-def fetch_SNVs(mutations, genome, region, meta):
-  SNVs = []
-  column_headings = [
-    'Chromosome'.lower(), 
-    'Start_Position'.lower(),
-    'End_Position'.lower(),
-    'Reference_Allele'.lower(), 
-    'Tumor_Seq_Allele1'.lower(), 
-    'Tumor_Seq_Allele2'.lower(), 
-    'Tumor_Sample_Barcode'.lower(),
-    'Variant_Type'.lower(), 
-    'ref_context' 
-  ]
-  column_heading_indices = fetch_column_heading_indices(meta['mutations'])
-  for row in mutations.fetch(region=region, parser=pysam.asTuple()):
-    mutation = {}
-    for column_heading in column_headings: 
-      try: 
-        mutation[column_heading] = row[column_heading_indices[column_heading]]
-      except KeyError: 
-        continue
-
-    if mutation['reference_allele'] == '-': continue # exclude INS
-    if len(mutation['reference_allele']) != 1: continue # exclude DEL, DNP, TNP, ONP
-    if mutation['tumor_seq_allele2'] not in {'A', 'T', 'G', 'C'}: continue # exclude DEL 
-
-    try: 
-      if mutation['reference_allele'] != mutation['tumor_seq_allele1']: # sanity check
-        print_json(mutation)
-        raise ValueError('Tumor allele 1 is not the same as reference allele') 
-      del mutation['tumor_seq_allele1']
-    except KeyError:
-      pass
-
-    start = int(mutation['start_position'])
-    mutation['position'] = start - 1
-    del mutation['start_position']
-
-    try: 
-      if start != int(mutation['end_position']): # sanity check for SNPs
-        print_json(mutation)
-        raise ValueError('SNPs must have equal start and end values') 
-      del mutation['end_position']
-    except KeyError:
-      pass
-
-    kmer = fetch_kmer_from_genome(genome, mutation['chromosome'], mutation['position'], meta['kmer_size'])
-    mutation['kmer'] = kmer
-    
-    if middle_base(kmer) != mutation['reference_allele'].upper(): # sanity check
-      print_json(mutation)
-      raise ValueError('Middle base of kmer does not match ref allele: {} {}'.format(
-        middle_base(kmer), 
-        mutation['reference_allele']
-      )) 
-    
-    try:
-      ref_context = mutation['ref_context'].upper() 
-      kmer_from_maf = fetch_kmer_from_sequence(ref_context, middle_index(ref_context), meta['kmer_size'])        
-      check_for_Ns(kmer_from_maf) # sanity check 
-      if kmer_from_maf != kmer: # sanity check
-        print_json(mutation)
-        raise ValueError('kmer from maf does not match kmer inferred from fasta') 
-      del mutation['ref_context']
-    except KeyError:
-      pass
-
-    try: 
-      if mutation['variant_type'] != 'SNP': # sanity check
-        print_json(mutation)
-        raise ValueError('variant_type is not SNP') 
-      del mutation['variant_type']
-    except KeyError:
-      pass
-
-    mutation['REF'] = mutation.pop('reference_allele')
-    mutation['ALT'] = mutation.pop('tumor_seq_allele2')
-
-    SNVs.append(mutation)
-  return SNVs
-

From 5aebf2a717f67dccb02ee5103624ebe64ed34930 Mon Sep 17 00:00:00 2001
From: Suchita Lulla <suchitalulla@gmail.com>
Date: Tue, 9 Nov 2021 20:51:18 -0700
Subject: [PATCH 7/9] fixed vcf bug

---
 predict-constraint/compute_mutation_counts.py |   7 +-
 report/constraintview                         |   8 +-
 report/constraintview.py                      |   8 +-
 report/constraintview.yaml                    |   4 +-
 report/get_coords.py                          |  11 +-
 report/glyphs.py                              |   4 +-
 utilities/fetch_SNVs.py                       | 108 ++++++++++++++++++
 7 files changed, 128 insertions(+), 22 deletions(-)
 create mode 100644 utilities/fetch_SNVs.py

diff --git a/predict-constraint/compute_mutation_counts.py b/predict-constraint/compute_mutation_counts.py
index 1bece36..93b496d 100644
--- a/predict-constraint/compute_mutation_counts.py
+++ b/predict-constraint/compute_mutation_counts.py
@@ -119,10 +119,8 @@ def compute_SNV_positions_frequencies(SNVs, filter_function):
   SNV_positions = [SNV['position'] for SNV in SNVs if filter_function(SNV['kmer'])]  
   # find frequency of each unique coordinate using Counter: 
   # https://stackoverflow.com/a/2162045/6674256  
-  #SNV_positions_frequencies = collections.Counter(SNV_positions)
-  SNV_positions_frequencies = [SNV['ac'] for SNV in SNVs if filter_function(SNV['kmer'])]
-  #return tuple(zip(*SNV_positions_frequencies.items()))
-  return (SNV_positions, SNV_positions_frequencies)
+  SNV_positions_frequencies = collections.Counter(SNV_positions)
+  return tuple(zip(*SNV_positions_frequencies.items()))
 
 def compute_lollipops(mutations, genome, region, model):
   SNVs = fetch_SNVs(mutations, genome, region, meta=model)
@@ -177,7 +175,6 @@ def parse_arguments():
 
 if __name__ == '__main__':
   args = parse_arguments() 
-
   
   print(
     json.dumps(
diff --git a/report/constraintview b/report/constraintview
index 5fce068..640f615 100755
--- a/report/constraintview
+++ b/report/constraintview
@@ -1,9 +1,7 @@
 #!/usr/bin/env bash
-###args: gff_path, model_path, gene_name, seqid (create)
-#config file, transcripts, outputfile (opt)
 
-config_file="constraintview.yaml"
-#transcripts="all"
+#config_file="constraintview.yaml"
+transcripts="all"
 output="plot.html"
 
 while [[ "$1" =~ ^- ]]; do 
@@ -17,5 +15,5 @@ while [[ "$1" =~ ^- ]]; do
 done
 
 cd ${CONSTRAINT_TOOLS}/report
-python create_constraint_txt.py constraintview.yaml
+python create_constraint_txt.py ${config_file}
 python constraintview.py ${config_file} ${transcripts} -o ${output}
\ No newline at end of file
diff --git a/report/constraintview.py b/report/constraintview.py
index 536d4fe..f36f05d 100755
--- a/report/constraintview.py
+++ b/report/constraintview.py
@@ -11,11 +11,11 @@
 from bokeh.plotting import figure, output_file, save
 from bokeh.layouts import column, row, gridplot
 from bokeh.models import ColumnDataSource, Range1d, HoverTool, LabelSet
-#import tabix
 import yaml
 from yaml.loader import SafeLoader
 
 def constraint_view_plot(plot_params, variant_params, user_line_params, transcript_dict, glyph_dict, axes, variant_ls, user_tracks, user_track_glyphs, user_lines, user_line_glyphs, title=''):
+
     project_coords.adjust_coordinates(transcript_dict['exons'], intron_size=plot_params['intron_size'])
     plot_height = plot_params['plot_height']    
     plot = figure(title=title, plot_width=1500, tools='tap,box_zoom,xpan,reset', plot_height=plot_height,min_border=0,#, toolbar_location=None,
@@ -40,6 +40,8 @@ def constraint_view_plot(plot_params, variant_params, user_line_params, transcri
             axes['count'].append(add_variant_axis(plot_params, variant_params, plot, 'Allele count', allele_counts, visible=True))
             axes['allele_frequency'].append(add_variant_axis(plot_params, variant_params, plot, 'Allele frequency',allele_frequencies, visible=False))
 
+    else: variant_params['add_variant_axis'] = False
+
     tooltips_features = [('Type','@feat_type'), ('Start (compact)', '@adj_start'), ('End (compact)', '@adj_end'), 
                       ('Start (chr)', '@true_start'), ('End (chr)', '@true_end'), ('Length', '@true_len')]
 
@@ -109,7 +111,6 @@ def parse_args():
 
     ### CONFIG ###
     config_file = args.config_file
-    print(config_file)
     # TODO what to do if config file doesn't have required params?
     if config_file[-5:] != '.yaml': raise ValueError('configuration file must be .yaml')
     with open(config_file) as f:
@@ -152,8 +153,7 @@ def parse_args():
 
 def constraint_view():
     plot_params, variant_params, user_track_params, user_line_params, transcript_IDs, output = parse_args()
-
-    # 'test.db' to make sure .db does not get overwritten during development    
+    # 'test.db' to make sure .db does not accidentally get overwritten during development    
     gff_db = gff_to_db(plot_params['gff_path'],plot_params['gff_path']+'test.db')
     
     gene_feature = get_gene_feature(gff_db, plot_params['gene_name'])
diff --git a/report/constraintview.yaml b/report/constraintview.yaml
index c4731f3..1568aec 100755
--- a/report/constraintview.yaml
+++ b/report/constraintview.yaml
@@ -6,9 +6,9 @@
 #variant_path: 'gnomad_v3_variants.bed'
 ###REMOTE PATHS
 gff_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/Homo_sapiens.GRCh38.104.gff3.db'
-#variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomAD_v3.1.1_ENSG00000075043_2021_09_16_16_02_28.csv'
+variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomAD_v3.1.1_ENSG00000075043_2021_09_16_16_02_28.csv'
 #variant_path: /scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/gnomad/v3/gnomad_v3_variants.sorted.bed.gz
-variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomad.exomes.r2.1.1.sites.20.vcf.bgz'
+#variant_path: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/gnomad.exomes.r2.1.1.sites.20.vcf.bgz'
 model_path: '/scratch/ucgd/lustre-work/quinlan/data-shared/constraint-tools/model.ptm.json' 
 ####Plot params
 gene_name: 'KCNQ2'
diff --git a/report/get_coords.py b/report/get_coords.py
index 57d8ac0..3a0a72d 100755
--- a/report/get_coords.py
+++ b/report/get_coords.py
@@ -18,8 +18,10 @@ def get_variants_vcf(vcf_path):
         import tabix #putting import here for now because it doesn't work on local machine
         tb = tabix.open(vcf_path)
         #TODO cast seqid in parse_args
-        for idx,r in enumerate(tb.query(str(seqid),start-1400000,end-1400000)):
-            variant_ls.append(dict(pos=int(r[1])+1400000, compact_pos=-1, ref=r[3], alt=r[4], #adding 1.4m bc this vcf is on old build
+        #for idx,r in enumerate(tb.query(str(seqid),start-1400000,end-1400000)):
+        for idx,r in enumerate(tb.query(str(seqid),start,end)):
+            #variant_ls.append(dict(pos=int(r[1])+1400000, compact_pos=-1, ref=r[3], alt=r[4], #adding 1.4m bc this vcf is on old build
+            variant_ls.append(dict(pos=int(r[1]), compact_pos=-1, ref=r[3], alt=r[4],
                               annotation=r[7].split(';')[-1].split('|')[1], severity=r[7].split(';')[-1].split('|')[2],
                               allele_count=int(r[7].split(';')[0].split('=')[1]),
                               allele_number=int(r[7].split(';')[1].split('=')[1]),
@@ -45,9 +47,8 @@ def get_variants_bed(bed_path):
         tb = tabix.open(bed_path)
         #TODO cast seqid in parse_args
         #for idx,r in enumerate(tb.query(str(seqid),start-1400000,end-1400000)):
-        for idx,r in enumerate(tb.query(str(seqid),start,end)):
-            #if idx<10: print(r)
-            variant_ls.append(dict(pos=int(r[1])+1400000, compact_pos=-1, ref=r[3], alt=r[4], #adding 1.4m bc this bed is on old build
+        for r in tb.query(str(seqid),start,end):
+            variant_ls.append(dict(pos=int(r[1]), compact_pos=-1, ref=r[3], alt=r[4], #adding 1.4m bc this bed is on old build
                              annotation=r[8], severity=variant_type(r[8]),
                              allele_count=-1,
                              allele_number=-1,
diff --git a/report/glyphs.py b/report/glyphs.py
index bd7f1c7..e39eecb 100755
--- a/report/glyphs.py
+++ b/report/glyphs.py
@@ -147,7 +147,9 @@ def add_UTR_glyph(plot_params, plot, UTRs, fill_alpha=0.4):
 def add_variant_glyph(plot_params, variant_params, plot, variant_ls, line_width=2):
     variant_ls = [v for v in variant_ls if v['compact_pos'] >= 0]
     N = len(variant_ls)
-    if N == 0: return None, None, [0], [0]
+    if N == 0: 
+        variant_params['add_variant_axis'] = False
+        return None, None, [0], [0]
     allele_counts = [v['allele_count'] for v in variant_ls]
     allele_numbers = [v['allele_number'] for v in variant_ls]
     allele_frequencies = [v['allele_frequency'] for v in variant_ls]
diff --git a/utilities/fetch_SNVs.py b/utilities/fetch_SNVs.py
new file mode 100644
index 0000000..de0019b
--- /dev/null
+++ b/utilities/fetch_SNVs.py
@@ -0,0 +1,108 @@
+# pysam API: 
+# https://github.com/pysam-developers/pysam/blob/b82cbcae22c088e64fdb58f8acaf1e9773c7b088/pysam/libctabix.pyx
+import pysam
+
+from column_headings import fetch_column_heading_indices
+from colorize import print_json
+from kmer import fetch_kmer_from_genome, fetch_kmer_from_sequence, middle_base, middle_index, check_for_Ns
+
+def fetch_SNVs(mutations, genome, region, meta):
+  SNVs = []
+  column_headings = [
+    #'Chromosome'.lower(), 
+    #'Start_Position'.lower(),
+    #'End_Position'.lower(),
+    #'Reference_Allele'.lower(), 
+    #'Tumor_Seq_Allele1'.lower(), 
+    #'Tumor_Seq_Allele2'.lower(), 
+    #'Tumor_Sample_Barcode'.lower(),
+    #'Variant_Type'.lower(), 
+    #'ref_context' 
+    'chrom', 'start', 'end', 'ref', 'alt', 'allele_count', 'variant_type'
+  ]
+  column_heading_indices = fetch_column_heading_indices(meta['mutations'])
+  #print('column_heading_indices',column_heading_indices)
+  for row in mutations.fetch(region=region, parser=pysam.asTuple()):
+    mutation = {}
+    for column_heading in column_headings: 
+      try: 
+        mutation[column_heading] = row[column_heading_indices[column_heading]]
+      except KeyError: 
+        continue
+    #if mutation['reference_allele'] == '-': continue # exclude INS
+    #print(mutation['start'])
+    if mutation['ref'] == '-': continue # exclude INS
+    #if len(mutation['reference_allele']) != 1: continue # exclude DEL, DNP, TNP, ONP
+    if len(mutation['ref']) != 1: continue
+    #if mutation['tumor_seq_allele2'] not in {'A', 'T', 'G', 'C'}: continue # exclude DEL
+    if mutation['alt'] not in {'A', 'T', 'G', 'C'}: continue
+    
+    ###I don't think we need this block for this file format?
+    #try: 
+      #if mutation['reference_allele'] != mutation['tumor_seq_allele1']: # sanity check
+    #    print_json(mutation)
+    #    raise ValueError('Tumor allele 1 is not the same as reference allele') 
+    #  del mutation['tumor_seq_allele1']
+    #except KeyError:
+    #  pass
+
+    #start = int(mutation['start_position'])
+    start = int(mutation['start'])
+    #mutation['position'] = start - 1
+    mutation['position'] = start
+    #del mutation['start_position']
+    del mutation['start']
+
+    try: 
+      #if start != int(mutation['end_position']): # sanity check for SNPs
+      if start != int(mutation['end'])-1: # sanity check for SNPs
+        print_json(mutation)
+        #raise ValueError('SNPs must have equal start and end values') 
+        raise ValueError('SNPs must start and end values 1 bp apart') 
+      #del mutation['end_position']
+      del mutation['end']
+    except KeyError:
+      pass
+
+    #kmer = fetch_kmer_from_genome(genome, mutation['chromosome'], mutation['position'], meta['kmer_size'])
+    kmer = fetch_kmer_from_genome(genome, mutation['chrom'], mutation['position'], meta['kmer_size'])
+    mutation['kmer'] = kmer
+    
+    #if middle_base(kmer) != mutation['reference_allele'].upper(): # sanity check
+    if middle_base(kmer) != mutation['ref'].upper(): # sanity check
+      print_json(mutation)
+      raise ValueError('Middle base of kmer does not match ref allele: {} {} {}'.format(
+        middle_base(kmer), 
+        kmer,
+        #mutation['reference_allele']
+        mutation['ref']
+      )) 
+    
+    try:
+      ref_context = mutation['ref_context'].upper() 
+      kmer_from_maf = fetch_kmer_from_sequence(ref_context, middle_index(ref_context), meta['kmer_size'])        
+      check_for_Ns(kmer_from_maf) # sanity check 
+      if kmer_from_maf != kmer: # sanity check
+        print_json(mutation)
+        raise ValueError('kmer from maf does not match kmer inferred from fasta') 
+      del mutation['ref_context']
+    except KeyError:
+      pass
+
+    try: 
+      #if mutation['variant_type'] != 'SNP': # sanity check
+      if mutation['feature_type'] != 'SNP': # sanity check
+        print_json(mutation)
+        raise ValueError('variant_type is not SNP') 
+      #del mutation['variant_type']
+      del mutation['feature_type']
+    except KeyError:
+      pass
+
+    #mutation['REF'] = mutation.pop('reference_allele')
+    mutation['REF'] = mutation.pop('ref')
+    #mutation['ALT'] = mutation.pop('tumor_seq_allele2')
+    mutation['ALT'] = mutation.pop('alt')
+
+    SNVs.append(mutation)
+  return SNVs
\ No newline at end of file

From fbabe8e8d0f82919f3aface23a6389b494a36bd1 Mon Sep 17 00:00:00 2001
From: Suchita Lulla <suchitalulla@gmail.com>
Date: Tue, 9 Nov 2021 21:13:17 -0700
Subject: [PATCH 8/9] updated README

---
 README.md             | 19 +++++++++++++++++++
 report/constraintview |  6 +++---
 2 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index b4f5b97..737e246 100644
--- a/README.md
+++ b/README.md
@@ -49,6 +49,8 @@ dashboard
       start a web app that visualizes observed and expected mutation counts as a function of genomic coordinate
 predict
       call genomic regions predicted to be under negative selection [not yet implemented]
+report
+      create .html plot displaying gene transcripts with introns compressed, observed and expected mutation counts, lollipops, tracks, and sequence coverage
 ```
 
 Required arguments for `train` are:
@@ -93,6 +95,23 @@ Optionally, the user may change this by specifying the `--model` argument:
       Path to a neutral model produced by the train sub-command (in json format). This model is used to compute the expected mutation counts in the visualization. 
 ```
 
+Required arguments for `report` are:
+
+```
+--config_file STR
+      Path to .yaml configuration file (example: reports/constraintview.yaml).
+--output_file STR
+      File name of output plot.
+```
+
+By default, the `report` subcommand plots all transcripts plus flattened-exons.
+Optionally, the user may change this by specifying the `--transcripts` argument:
+
+```
+--transcripts STR
+      Specifies which transcripts to plot. Can be 'all' for all transcripts or '['<transcript_name_1>', '<transcript_name_2>', ...]' for specific transcripts.
+```
+
 ## Input Data
 
 Assuming one has access to the protected environment on the CHPC at University of Utah, 
diff --git a/report/constraintview b/report/constraintview
index 640f615..444a463 100755
--- a/report/constraintview
+++ b/report/constraintview
@@ -2,13 +2,13 @@
 
 #config_file="constraintview.yaml"
 transcripts="all"
-output="plot.html"
+#output="plot.html"
 
 while [[ "$1" =~ ^- ]]; do 
   case $1 in
     --config_file ) shift; [[ ! $1 =~ ^- ]] && config_file=$1;;
     --transcripts ) shift; [[ ! $1 =~ ^- ]] && transcripts=$1;;
-    --output ) shift; [[ ! $1 =~ ^- ]] && output=$1;;
+    --output_file ) shift; [[ ! $1 =~ ^- ]] && output=$1;;
     *) error "$0: $1 is an invalid flag"; exit 1;;
   esac 
   shift
@@ -16,4 +16,4 @@ done
 
 cd ${CONSTRAINT_TOOLS}/report
 python create_constraint_txt.py ${config_file}
-python constraintview.py ${config_file} ${transcripts} -o ${output}
\ No newline at end of file
+python constraintview.py ${config_file} ${transcripts} -o ${output_file}
\ No newline at end of file

From 6ea13d06303891644de3d730e65311d20b7cbfb0 Mon Sep 17 00:00:00 2001
From: Suchita Lulla <suchitalulla@gmail.com>
Date: Tue, 9 Nov 2021 22:59:03 -0700
Subject: [PATCH 9/9] moved coverage files to scratch

---
 report/KCNQ2_coverage.bedgraph | 1763 --------------------------------
 report/constraintview          |    4 +-
 report/constraintview.yaml     |    2 +-
 3 files changed, 3 insertions(+), 1766 deletions(-)
 delete mode 100755 report/KCNQ2_coverage.bedgraph

diff --git a/report/KCNQ2_coverage.bedgraph b/report/KCNQ2_coverage.bedgraph
deleted file mode 100755
index 61a8446..0000000
--- a/report/KCNQ2_coverage.bedgraph
+++ /dev/null
@@ -1,1763 +0,0 @@
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-20	63547776	63547778	0.9
-20	63547799	63547801	0.3
-20	63547832	63547834	0.6
-20	63547900	63547903	0.9
-20	63547931	63547932	0.6
-20	63547974	63547985	0.6
-20	63548044	63548045	0.7
-20	63548070	63548075	1.0
-20	63548124	63548127	0.2
-20	63548188	63548197	0.8
-20	63548246	63548255	0.9
-20	63548316	63548318	0.9
-20	63548382	63548383	0.9
-20	63548459	63548460	0.9
-20	63548524	63548731	0.4
-20	63548775	63548776	0.5
-20	63548845	63548848	1.0
-20	63548887	63548891	0.9
-20	63548952	63548953	0.7
-20	63549033	63549946	0.9
-20	63549990	63550005	0.7
-20	63550022	63550024	0.7
-20	63550063	63550064	0.6
-20	63550099	63550104	0.4
-20	63550161	63550166	0.8
-20	63550217	63550218	0.8
-20	63550262	63550263	0.6
-20	63550263	63550265	0.7
-20	63550332	63550337	0.7
-20	63550362	63550365	0.9
-20	63550400	63550413	0.9
-20	63550441	63550442	1.0
-20	63550486	63550494	0.3
-20	63550511	63550513	0.7
-20	63550548	63550549	0.6
-20	63550574	63550577	0.9
-20	63550607	63550617	0.3
-20	63550642	63550697	0.2
-20	63550756	63551592	0.6
-20	63551654	63551656	0.9
-20	63551713	63551719	0.8
-20	63551774	63551784	0.6
-20	63551878	63551881	1.0
-20	63551927	63553135	0.7
-20	63553144	63553148	0.6
-20	63553169	63553170	0.9
-20	63553219	63553226	0.4
-20	63553282	63553286	0.3
-20	63553343	63553344	0.6
-20	63553353	63553355	0.9
-20	63553380	63553383	1.0
-20	63553388	63553390	0.8
-20	63553417	63553424	0.4
-20	63553465	63553474	0.5
-20	63553534	63553535	1.0
-20	63553574	63553610	0.8
-20	63553665	63553666	0.7
-20	63553735	63553737	0.6
-20	63553794	63553799	0.5
-20	63553812	63553813	0.6
-20	63553848	63553849	0.9
-20	63553858	63553859	0.8
-20	63553906	63553908	0.9
-20	63553917	63553923	0.6
-20	63553983	63553984	1.0
-20	63554014	63554019	0.8
-20	63554050	63554053	0.8
-20	63554092	63554096	0.7
-20	63554131	63554137	0.7
-20	63554203	63554204	0.7
-20	63554232	63554233	0.9
-20	63554263	63554264	0.8
-20	63554321	63554324	0.8
-20	63554355	63554356	0.6
-20	63554415	63554416	0.5
-20	63554472	63554483	0.9
-20	63554532	63554535	1.0
-20	63554543	63554544	0.8
-20	63554593	63554594	0.6
-20	63554655	63554665	0.9
-20	63554725	63554757	0.7
-20	63554774	63554780	0.7
-20	63554841	63554880	1.0
-20	63554941	63554945	0.7
-20	63554992	63555055	0.2
-20	63555102	63555116	0.9
-20	63555171	63555176	0.7
-20	63555241	63555247	1.0
-20	63555322	63555333	0.4
-20	63555380	63555386	0.7
-20	63555425	63555426	0.8
-20	63555457	63555458	0.9
-20	63555497	63555606	0.6
-20	63555642	63555648	0.9
-20	63555725	63556295	0.7
-20	63556316	63556416	0.4
diff --git a/report/constraintview b/report/constraintview
index 444a463..bfaf967 100755
--- a/report/constraintview
+++ b/report/constraintview
@@ -2,13 +2,13 @@
 
 #config_file="constraintview.yaml"
 transcripts="all"
-#output="plot.html"
+output="plot.html"
 
 while [[ "$1" =~ ^- ]]; do 
   case $1 in
     --config_file ) shift; [[ ! $1 =~ ^- ]] && config_file=$1;;
     --transcripts ) shift; [[ ! $1 =~ ^- ]] && transcripts=$1;;
-    --output_file ) shift; [[ ! $1 =~ ^- ]] && output=$1;;
+    --output_file ) shift; [[ ! $1 =~ ^- ]] && output_file=$1;;
     *) error "$0: $1 is an invalid flag"; exit 1;;
   esac 
   shift
diff --git a/report/constraintview.yaml b/report/constraintview.yaml
index 1568aec..6ae81d2 100755
--- a/report/constraintview.yaml
+++ b/report/constraintview.yaml
@@ -89,7 +89,7 @@ Coverage:
     lines:
         Coverage:
             #line params
-            filepath: 'KCNQ2_coverage.bedgraph'
+            filepath: '/scratch/ucgd/lustre-work/quinlan/u6038618/constraint-tools/data/KCNQ2_coverage.bedgraph'
             color: '#00916E'
             alpha: 0.5
             fill_area: True