Release 0.2.0

HISTORY.rst

@@ -2,6 +2,39 @@
 
 History
 =======
+0.2.0 (2015-10-15)
+------------------
+**riboplot**
+
+* Support for color schemes - options: default, colorbrewer, rgb, greyorfs.
+* Plot changes - colored, light background for ORF architecture, legend moved down.
+* Image DPI change 300 |srarr| 600.
+* Sample scripts to plot multiple transcripts and multiple color schemes.
+
+**ribocount**
+
+* Ability to output read counts in 5'(``-v``) and 3'(``-r``) leader region.
+
+Bugfixes
+
+1. Report error if a bam index could not be generated (ex. bam sorted using 
+   reference names instead of chromosome coordinates).
+2. No start/stop values when transcript sequences are in lower case.
+
+Tests
+
+* Split into three different files.
+* Updated test configuration.
+
+Minor
+
+* XML wrapper changes - remove 'leader', add help text and output label change [ribocount].
+* Remove unused pysam import [riboplot].
+* Replace doc includes with sym links (breaks Galaxy toolshed otherwise).
+* Updated CSS/Table styles (removed number column from table).
+* y limit is now 1.25x [riboplot].
+* Removed line width on bars [riboplot].
+
 0.1.1 (2015-09-08)
 ------------------
 * Remove invalid Python 3 version (whl).
@@ -12,3 +45,6 @@ History
 0.1.0 (2015-08-24)
 ------------------
 * First release on PyPI.
+
+.. substitutions  
+.. |srarr|    unicode:: U+02192 .. RIGHTWARDS ARROW

README.rst

@@ -22,5 +22,5 @@ There are two programs in the package:
 
 Free software: GPL license.
 
-Documentation: https://riboplot.readthedocs.org.
+Documentation: http://pythonhosted.org/riboplot.
 

docs/conf.py

@@ -15,17 +15,6 @@
 
 import sys
 import os
-# To get the docs to build on readthedocs.org
-from mock import Mock as MagicMock
-
-class Mock(MagicMock):
-    @classmethod
-    def __getattr__(cls, name):
-        return Mock()
-
-MOCK_MODULES = ['matplotlib']
-sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
-
 
 # If extensions (or modules to document with autodoc) are in another
 # directory, add these directories to sys.path here. If the directory is

docs/usage.rst

@@ -32,7 +32,7 @@ and the Ribo-Seq/RNA-Seq alignment (BAM).
 ++++++++++++++++++++++++++++++++++++++++++++
 If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage.
 
-5. Read lengths to consider [Optional] (Integer - 0 or greater)
+5. Read lengths to consider [optional] (Integer - 0 or greater)
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 If this option is provided, only Ribo-Seq data of the given length is considered.
 
@@ -53,6 +53,7 @@ The open reading frame architecture appears below the plot with start (ATG) and
 The color codes are start (white) and stop (dark gray).
 
 .. image:: ../images/riboplot.png
+   :width: 80 %
 
 2. RiboSeq read counts (CSV)
 ++++++++++++++++++++++++++++
@@ -63,44 +64,38 @@ Command line
 ............
 ``riboplot`` can also be run on the command line. The usage is ::
 
-    usage: riboplot [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA -t TEXT
-                    [-n RNA_FILE] [-l INTEGER] [-s INTEGER] [-m HTML_FILE]
-                    [-o OUTPUT_PATH] [-d]
+    riboplot [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA -t TEXT
+             [-n RNA_FILE] [-l INTEGER] [-s INTEGER] 
+             [-c {default,colorbrewer,rgb,greyorfs}] [-m HTML_FILE]
+             [-o OUTPUT_PATH] [-d]
 
-    Plot and output read counts for a single transcript
+Plot and output read counts for a single transcript
 
-    optional arguments:
-    -h, --help
-        show this help message and exit
+**required arguments**:
+    -b RIBO_FILE, --ribo_file RIBO_FILE
+        Ribo-Seq alignment file in BAM format
+    -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA
+        FASTA format file of the transcriptome
+    -t TEXT, --transcript_name TEXT
+        Transcript name
 
+**optional arguments**:
+    -h, --help  show this help message and exit
     -n RNA_FILE, --rna_file RNA_FILE
         RNA-Seq alignment file (BAM)
-
     -l INTEGER, --read_length INTEGER
         Read length to consider (default: None)
-
     -s INTEGER, --read_offset INTEGER
         Read offset (default: 0)
-
+    -c COLOR_SCHEME, --color_scheme COLOR_SCHEME                
+         Color scheme to use (default: default). Other options are colorbrewer, rgb, greyorfs
     -m HTML_FILE, --html_file HTML_FILE
         Output file for results (HTML)
-
     -o OUTPUT_PATH, --output_path OUTPUT_PATH
         Files are saved in this directory
-
     -d, --debug
         Flag. Produce debug output
 
-    required arguments:
-    -b RIBO_FILE, --ribo_file RIBO_FILE
-        Ribo-Seq alignment file in BAM format
-
-    -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA
-        FASTA format file of the transcriptome
-
-    -t TEXT, --transcript_name TEXT
-        Transcript name
-
 RiboCount
 ---------
 Output read counts for all transcripts in an alignment.
@@ -127,6 +122,12 @@ If this option is provided, only Ribo-Seq data of the given length is considered
 +++++++++++++++++++++++++++++++++++++++++++++
 If this option is provided, this offset is added to the read alignment positions.
 
+5. Restrict read counts
++++++++++++++++++++++++
+Choose whether to output read counts for the entire transcript or restrict read counts to the 5' or 3' region of the longest ORF.
+Default start (ATG) and stop codons ('TAG', 'TGA', 'TAA') are used to identify the longest ORF in 3 frames.
+
+
 Output
 ......
 Read counts for all transcripts in the alignment (ZIP)
@@ -135,45 +136,40 @@ The output file ``ribocount_output.zip`` should first be uncompressed. This will
 a folder called ``ribocount_output``. Open ``index.html`` in a web browser to view the results of ribocount.
 
 Total reads for each transcript will be displayed in a table along with the name of the transcript and a link
-to the CSV file containing the read counts in 3 frames for each position in the transcript.
+to the CSV file containing the read counts in 3 frames for each position in the transcript. If 5' or 3' counts
+are requested, an extra column will be present with reads in these regions.
 
 .. image:: ../images/ribocount.png
 
 Command line
 ............
 ``ribocount`` can also be run on the command line. The usage is ::
 
-    usage: ribocount [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER]
-    [-s INTEGER] [-m HTML_FILE] [-o OUTPUT_PATH] [-d]
+    ribocount [-h] -b RIBO_FILE -f TRANSCRIPTOME_FASTA [-l INTEGER]
+                    [-s INTEGER] [-v | -r] [-m HTML_FILE] [-o OUTPUT_PATH]
+                    [-d]
 
     Output read counts for all transcripts
 
-    optional arguments:
-
-        -h, --help            show this help message and exit
-
-        -l INTEGER, --read_length INTEGER
-            Read length to consider (default: None)
-
-        -s INTEGER, --read_offset INTEGER
-            Read offset (default: 0)
-
-        -m HTML_FILE, --html_file HTML_FILE
-
-            Output file for results (HTML)
-
-        -o OUTPUT_PATH, --output_path OUTPUT_PATH
-            Files are saved in this directory
-
-        -d, --debug           Flag. Produce debug output
-
-    required arguments:
-
-        -b RIBO_FILE, --ribo_file RIBO_FILE
-            Ribo-Seq alignment file in BAM format
+**required arguments**:
+    -b RIBO_FILE, --ribo_file RIBO_FILE
+        Ribo-Seq alignment file in BAM format
+    -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA
+        FASTA format file of the transcriptome
 
-        -f TRANSCRIPTOME_FASTA, --transcriptome_fasta TRANSCRIPTOME_FASTA
-            FASTA format file of the transcriptome
+**optional arguments**:
+    -h, --help            show this help message and exit
+    -l INTEGER, --read_length INTEGER
+        Read length to consider (default: None)
+    -s INTEGER, --read_offset INTEGER
+        Read offset (default: 0)
+    -v, --count_five      Flag. Output reads in 5' region
+    -r, --count_three     Flag. Output reads in 3' region
+    -m HTML_FILE, --html_file HTML_FILE
+        Output file for results (HTML)
+    -o OUTPUT_PATH, --output_path OUTPUT_PATH
+        Files are saved in this directory
+    -d, --debug           Flag. Produce debug output
 
 .. links
 .. _RiboGalaxy: http://ribogalaxy.ucc.ie

requirements.txt

@@ -1,3 +1,2 @@
-mock==1.0.1
 matplotlib==1.4.3
 pysam==0.8.3

riboplot/__init__.py

@@ -2,4 +2,4 @@
 
 __author__ = 'Vimalkumar Velayudhan'
 __email__ = '[email protected]'
-__version__ = '0.1.1'
+__version__ = '0.2.0'

riboplot/riboplot.py

@@ -120,7 +120,7 @@ def get_color_palette(scheme):
     """
     color_schemes = {
         'default': {
-            'frames': ['tomato', 'limegreen', 'deepskyblue'], 'background': '#f5f5f5',
+            'frames': ['tomato', 'limegreen', 'deepskyblue'], 'background': '#fafafa',
             'color': '#616161', 'ticks': '#757575', 'start': '#ffffff', 'stop': '#919191',
             'rna': '#e0e0e0', 'axis': '#e0e0e0', 'grey': '#bdbdbd'
         },

setup.py

@@ -14,15 +14,15 @@
 with open('HISTORY.rst') as history_file:
     history = history_file.read().replace('.. :changelog:', '')
 
-requirements = ['matplotlib', 'pysam', 'mock==1.0.1']
+requirements = ['matplotlib', 'pysam']
 
 test_requirements = [
     # TODO: put package test requirements here
 ]
 
 setup(
     name='riboplot',
-    version='0.1.1',
+    version='0.2.0',
     description="Plot read counts of RiboSeq data from BAM format alignment files",
     long_description=readme + '\n\n' + history,
     author="Vimalkumar Velayudhan",
@@ -39,8 +39,9 @@
     zip_safe=False,
     keywords='riboplot',
     classifiers=[
-        'Development Status :: 2 - Pre-Alpha',
-        'Intended Audience :: Developers',
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Science/Research',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
         'License :: OSI Approved :: GNU General Public License (GPL)',
         'Natural Language :: English',
         "Programming Language :: Python :: 2",