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ngs_primerplex.kv
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ScreenManager:
id: screen_manager
MenuScreen:
id: menu_screen
name: 'MenuScreen'
manager: 'screen_manager'
SettingsScreen:
id: settings
name: 'SettingsScreen'
manager: 'screen_manager'
ExtractRegions:
id: extract_regions
name: 'ExtractRegions'
manager: 'screen_manager'
DesignPrimers:
id: design_primers
name: 'DesignPrimers'
manager: 'screen_manager'
AddAdapters:
id: add_adapters
name: 'AddAdapters'
manager: 'screen_manager'
ConvertToDraft:
id: convert_to_draft
name: 'ConvertToDraft'
manager: 'screen_manager'
<MenuScreen>:
id:menu_screen
BoxLayout:
orientation:'vertical'
spacing:20
padding:(10,5,10,10)
canvas:
Color:
rgba:0.8,0.8,0.8,1
Rectangle:
pos:self.pos
size:self.size
BoxLayout:
orientation:'vertical'
size_hint:1,0.05
BoxLayout:
orientation:'horizontal'
spacing:20
size_hint:1,1
Button:
text:'Settings'
size_hint:0.2,1
pos_hint:{'x':0,'y':0}
on_press:app.root.current='SettingsScreen'
Button:
id:download_button
text:'Download NGS-PrimerPlex'
size_hint:0.4,1
on_press:menu_screen.download_ngs_primerplex()
Button:
id:prepare_ref_button
text:'Prepare hg19 reference'
size_hint:0.4,1
on_press:menu_screen.prepare_reference()
BoxLayout:
orientation:'horizontal'
spacing:20
size_hint:1,0.1
Label:
size_hint:0.2,1
color:0,0,0,1
font_size:18
Label:
id:download_status
size_hint:0.4,1
color:0,0,0,1
font_size:18
Label:
id:prepare_ref_status
size_hint:0.4,1
color:0,0,0,1
font_size:18
Button:
id:extract_regions_menu_button
canvas.before:
Color:
rgba:0,0,1,1
Rectangle:
pos:self.pos
size:self.size
bold:True
background_normal:''
background_color:0.15,0.35,0.54,1
text:'Extract regions'
size_hint:0.5,0.3
pos_hint:{'x':0.25,'y':0}
on_press:app.root.current='ExtractRegions'
Button:
id:design_primers_menu_button
canvas.before:
Color:
rgba:0,0,1,1
Rectangle:
pos:self.pos
size:self.size
bold:True
background_normal:''
background_color:0.15,0.35,0.54,1
text:'Design primers'
size_hint:0.5,0.3
pos_hint:{'x':0.25,'y':0}
on_press:app.root.current='DesignPrimers'
Button:
id:add_adapters_menu_button
canvas.before:
Color:
rgba:0,0,1,1
Rectangle:
pos:self.pos
size:self.size
bold:True
background_normal:''
background_color:0.15,0.35,0.54,1
text:'Add adapters'
size_hint:0.5,0.3
pos_hint:{'x':0.25,'y':0}
on_press:app.root.current='AddAdapters'
Button:
id:convert_to_draft_menu_button
canvas.before:
Color:
rgba:0,0,1,1
Rectangle:
pos:self.pos
size:self.size
bold:True
background_normal:''
background_color:0.15,0.35,0.54,1
text:'Convert to draft-primers'
size_hint:0.5,0.3
pos_hint:{'x':0.25,'y':0}
on_press:app.root.current='ConvertToDraft'
<SettingsScreen>:
id:settings
BoxLayout:
orientation:'vertical'
canvas:
Color:
rgba:0.8,0.8,0.8,1
Rectangle:
pos:self.pos
size:self.size
# All parts of settings
BoxLayout:
orientation:'horizontal'
padding:(10,10,10,0)
spacing:20
# Amplicon and primer settings
BoxLayout:
orientation:'vertical'
size_hint:0.33,1
Label:
text:'Amplicon and primer settings'
size_hint:1,1
color:0,0,0,1
bold:True
# Minimal amplicon length
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Min. amplicon length, bp'
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:minampllen
text:'100'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Optimal amplicon length
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Optimal amplicon length, bp'
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:optampllen
text:'110'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Maximal amplicon length
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Max. amplicon length, bp'
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:maxampllen
text:'110'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Minimal primer length
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Min. primer length'
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:minprimerlen
text:'16'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Optimal primer length
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Optimal primer length'
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:optprimerlen
text:'23'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Maximal primer length
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Max. primer length'
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:maxprimerlen
text:'28'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Minimal primer melt
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Min. primer melt, '+u'\N{DEGREE SIGN}'+'C'
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:minprimermelt
text:'60'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Optimal primer melt
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Optimal primer melt, '+u'\N{DEGREE SIGN}'+'C'
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:optprimermelt
text:'64'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Maximal primer melt
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Max. primer melt, '+u'\N{DEGREE SIGN}'+'C'
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:maxprimermelt
text:'68'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Minimal primer GC
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Min. primer GC, %'
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:minprimergc
text:'20'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Optimal primer GC
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Optimal primer GC, %'
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:optprimergc
text:'40'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Maximal primer GC
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Max. primer GC, %'
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:maxprimergc
text:'80'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Minimal primer 3'-end GC
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Min. GC at primer 3'-end"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:minprimerendgc
text:'0'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Optimal primer 3'-end GC
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Opt. GC at primer 3'-end"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:optprimerendgc
text:'2'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Maximal primer 3'-end GC
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Max. GC at primer 3'-end"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:maxprimerendgc
text:'5'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Maximal primer polyN
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Max. primer polyN length'
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:maxprimerpolyn
text:'8'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Switch for auto-adjust
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:'Auto-adjust parameters'
color:0,0,0,1
size_hint:0.8,1
halign:'left'
valign:'center'
text_size:self.size
Switch:
id:autoadjust
size_hint:0.2,1
active:False
pos_hint:{'x':0,'y':0}
# Four groups:
# - Interaction inside one pair
# - NonTargets
# - SNPs
# - Embedded PCR
BoxLayout:
orientation:'vertical'
size_hint:0.33,1
padding:(10,0,0,0)
canvas.before:
Color:
rgba:0.5,0.5,0.5,1
Line:
width: 1
rectangle: self.x, self.y, 1, self.height
Label:
text:'Interactions in one primer pair'
size_hint:1,1
color:0,0,0,1
bold:True
# Maximal primer complementary end Th
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Max. primer dimer Th with hybr. 3'-end"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:maxprimercomplendth
text:'25'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Maximal primer complementary any Th
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Max. primer dimer Th"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:maxprimercomplanyth
text:'35'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Maximal primer hairpin Th
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Max. primer hairpin Th"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:maxprimerhairpinth
text:'40'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Non-target hybridizations
Label:
text:'Non-target hybridizations'
size_hint:1,1
color:0,0,0,1
bold:True
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Max. diff. between primer and reference"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:subst
text:'2'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Maximal primer non target hybridizations
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Max. primer non-target sites"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:maxprimernonspec
text:'10000'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Maximal non-target amplicon length to check
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Max. non-target amplicon length"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:maxnonspeclen
text:'200'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# SNPs
Label:
text:'Covering SNPs'
size_hint:1,1
color:0,0,0,1
bold:True
# Minimal SNP frequency
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Min. SNP frequency, %"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:freq
text:'1'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'float'
pos_hint:{'x':0,'y':0}
write_tab: False
# Number of nucleotides from 3'-end
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Nucleotides at 3'-end to check for covering SNP"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:nucs
text:'0'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Embedded PCR
Label:
text:'Embedded PCR'
size_hint:1,1
color:0,0,0,1
bold:True
# Minimal primer shift
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Min. ext. primer shift"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:minprimershift
text:'5'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Optimal external length
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Opt. ext. amplicon length"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:optextampllen
text:'150'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Maximal external length
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Max. ext. amplicon length"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:maxextampllen
text:'150'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Two groups and buttons:
# - Multiplexing
# - Thermodynamics
# - Load
# - Save
BoxLayout:
orientation:'vertical'
size_hint:0.33,1
padding:(10,0,0,0)
canvas.before:
Color:
rgba:0.5,0.5,0.5,1
Line:
width: 1
rectangle: self.x, self.y, 1, self.height
Label:
text:'Multiplexing'
size_hint:1,1
color:0,0,0,1
bold:True
# Maximal overlap
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Max. overlap of sequenced regions"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:maxoverlap
text:'50'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Primer number to design for 1 locus
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Primer pairs to design for 1 locus"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:primernum1
text:'50'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Tries to get best combination
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Tries number to get best comb."
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:tries
text:'10000'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Return variants number
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Variants number to return"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:returnvariantsnum
text:'10'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'int'
pos_hint:{'x':0,'y':0}
write_tab: False
# Minimal dimer dG1 in multiplexes
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Min. dG with linked 3'-ends"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:minmultdimerdg1
text:'-6'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'float'
pos_hint:{'x':0,'y':0}
write_tab: False
# Minimal dimer dG2 in multiplexes
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Min. dG without linked 3'-ends"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:minmultdimerdg2
text:'-10'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'float'
pos_hint:{'x':0,'y':0}
write_tab: False
# Thermodynamical parameters
Label:
text:'Thermodynamical parameters'
size_hint:1,1
color:0,0,0,1
bold:True
# Monovalent cations
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Conc. of monovalent cations, mM"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:mv
text:'50'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'float'
pos_hint:{'x':0,'y':0}
write_tab: False
# Divalent cations
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Conc. of divalent cations, mM"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:dv
text:'3'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'float'
pos_hint:{'x':0,'y':0}
write_tab: False
# dNTP concentration
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"dNTP concentration, mM"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:dntp
text:'0.8'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'float'
pos_hint:{'x':0,'y':0}
write_tab: False
# primer concentration
BoxLayout:
size_hint:1,1
orientation:'horizontal'
Label:
text:"Primer concentration, nM"
color:0,0,0,1
size_hint:0.77,1
halign:'left'
valign:'center'
text_size:self.size
TextInput:
id:primerconc
text:'250'
hint_text_color:0,0,0,1
size_hint:0.23,1
input_filter:'float'
pos_hint:{'x':0,'y':0}
write_tab: False
# Save button
Button:
text:'Save settings'
on_press:settings.show_save()
size_hint_y:None
height:dp(40)
# Load button
Button:
text:'Load settings'
on_press:settings.show_load()
size_hint_y:None
height:dp(40)
Button:
text:'< Back to Main menu'
on_press:app.root.current='MenuScreen'
size_hint_y:None
height:dp(40)
<ExtractRegions>:
id:extract_regions
BoxLayout:
orientation:'vertical'
canvas.before:
Color:
rgba:0.8,0.8,0.8,1
Rectangle:
pos:self.pos
size:self.size
BoxLayout:
orientation:'horizontal'
size_hint:1,1
spacing:20
BoxLayout:
orientation:'vertical'
spacing:20
size_hint:0.4,1
padding:(10,10,0,0)
# Table with genes and their parts
GridLayout:
id:genes_table
canvas.before:
Color:
rgba:0.5,0.5,0.5,1
Rectangle:
pos:self.pos
size:self.size
Line:
width: 2
rectangle: self.x, self.y, self.width, self.height
spacing:2
cols:3
rows:2
size_hint:1,0.2
# Label for gene column