Mercurial > repos > proteore > proteore_venn_diagram
changeset 11:958eb2ea02aa draft default tip
"planemo upload commit 00cab92333b0338cb86ff78b5bbc1b6d26621012-dirty"
author | proteore |
---|---|
date | Wed, 12 May 2021 16:48:05 +0000 |
parents | e744a43171ff |
children | |
files | test-data/Venn_diagram_html.html test-data/Venn_text_output.txt venn_diagram.py venn_diagram.xml |
diffstat | 4 files changed, 333 insertions(+), 166 deletions(-) [+] |
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--- a/test-data/Venn_diagram_html.html Tue Jan 14 09:14:27 2020 -0500 +++ b/test-data/Venn_diagram_html.html Wed May 12 16:48:05 2021 +0000 @@ -62,9 +62,9 @@ } </style> - <script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script> - <script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script> - <script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script> + <script type="text/javascript" src="https://code.jquery.com/jquery-2.1.3.min.js"></script> + <script type="text/javascript" src="https://code.highcharts.com/4.1.4/highcharts.js"></script> + <script type="text/javascript" src="https://code.highcharts.com/4.1.4/modules/exporting.js"></script> <script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script> <script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script> <script 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"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], "ABC": ["P00338", "P00738", "P01871", "P02768", "P02788", "P04083", "P04406", "P05089", "P06396", "P07339", "P07355", "P07900", "P10599", "P15924", "P25311", "P27482", "P31025", "P31947", "P61626", "P63104", "P68871", "P80188", "Q01469", "Q02413", "Q08188", "Q86YZ3", "Q96P63", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""]}, "values": {"A": 59, "B": 71, "C": 80, "AB": 14, "AC": 51, "BC": 9, "ABC": 27}}], "displayStat": "true", "displaySwitch": "true", "shortNumber": "true"} ; $(document).ready(function(){ $('#example').jvenn(jvenn_data); }); @@ -152,7 +152,7 @@ 'nb_seq_ini': 100000 } */ - //var by_samples_results =Â ###SAMPLES_RESULTS### ; + //var by_samples_results = ###SAMPLES_RESULTS### ; /* Example: { 'sampleA':{ @@ -172,7 +172,7 @@ } } */ - //var by_filters_results =Â ###FILTERS_RESULTS### ; + //var by_filters_results = ###FILTERS_RESULTS### ; /* Example: [ {'filters':['filterA'], 'count': 10},
--- a/test-data/Venn_text_output.txt Tue Jan 14 09:14:27 2020 -0500 +++ b/test-data/Venn_text_output.txt Wed May 12 16:48:05 2021 +0000 @@ -1,81 +1,228 @@ -Lacombe Bredberg Mucilli Mucilli_Bredberg Lacombe_Bredberg Lacombe_Mucilli_Bredberg Lacombe_Mucilli -P0DMV9 P04217 Q7Z794 Q13835 P02787 P02768 P08779 -Q9Y6R7 P02649 P51149 P01023 P01833 P10599 P04259 -P30740 Q7Z351 P17900 P59665 P01625 P07355 O75223 -P68363 P08758 Q96KK5 Q15517 P22528 Q01469 P47756 -O75635 Q9UBC9 P10809 P05109 Q9UGM3 P68871 P06733 -O60911 P02760 O43175 P60709 Q96DA0 P07900 P20933 -P61160 O95436 Q6ZVX7 P62805 P02763 P15924 Q9NZH8 -Q15828 P02647 P01861 Q5D862 P61916 P25311 P09211 -P23284 P15814 P14174 P07737 P01009 Q86YZ3 P04792 -P20930 Q9NSK0 P01593 P12273 P05089 P36952 -P01860 P01717 Q15365 Q13867 Q08188 P01040 -Q96FX8 P04117 P37802 P01765 P04406 P60174 -P62937 Q13885 P29373 P01036 P07339 P26641 -Q15149 P01591 P30050 P01011 P06396 P14618 -P25705 O95613 Q6E0U4 P00338 P31944 -P19971 P01880 P23526 P61626 Q8N1N4 -O75342 P04233 Q13748 P04083 P04075 -Q92820 P01598 P05120 Q02413 P14923 -P25788 P01621 Q14134 P27482 Q8WVV4 -Q9HCY8 Q9UL77 P68431 P01871 O75369 -P19012 P05362 P35527 P80188 P00558 -Q8TAX7 P01024 Q5XKE5 P31947 P19013 -P42357 Q86SJ6 O15523 P31025 Q5T750 -P50395 P12429 P25787 Q96P63 P14735 -P01766 P43652 P22392 P63104 P47929 -P40121 P22897 P49189 P00738 Q06830 -P04080 P06313 P61978 P02788 P29508 -Q9HC84 B4E1Z4 P32119 P68371 -P59998 P01008 Q5VVQ6 Q9NZT1 -P23396 A2IPI6 Q8IW75 P11142 -P00491 P02790 P01620 P40926 -P62258 P61769 P02671 P01876 -P01623 P00450 P62244 P58107 -P31151 Q08380 P0CG48 P01834 -Q6P4A8 P02751 P02675 P18206 -P63261 Q8NF17 Q9Y277 Q04695 -P01877 Q14624 P02679 P08865 -P09228 P0C0L5 P02533 P13646 -P48637 P0C0L4 Q9Y337 P02545 -P07858 Q9UL83 P12035 P04040 -P07384 P08238 P52907 P13639 -P06870 P02766 P35321 P05090 -Q9UI42 Q9UL86 P13489 Q6KB66 -P35579 P02774 P29401 P01857 -P13473 P05155 P04264 Q6UWP8 -P62987 P11686 Q14210 Q9UIV8 -P04745 P01622 P28074 Q9C075 -P49720 Q6N093 P40925 O43707 -P11279 P04637 P28070 P11021 -P18510 Q96S96 P28072 P31949 -Q14574 P62807 Q14CN4 P60842 -P02538 P23528 Q9Y3R4 -P48594 P10909 P13647 -A8K2U0 A4F255 P54652 -P09972 P00734 Q08554 -O95274 P19827 P08107 -P01037 Q16378 P30041 -P0CG05 P01714 P06702 -P00441 P11217 O43790 - A0A0U1RVJ5 Q96QA5 - P01617 P23490 - P01611 P22735 - P04196 P13645 - P01613 P17931 - P02747 Q3ZCW2 - P80748 P68104 - A0N5G5 P06576 - Q8IWL2 Q5T749 - Q9BYE4 P05091 - P06681 O60814 - Q6MZX7 P37837 - P22531 - P03973 - P63167 - P05783 - P50990 - P15880 - P35908 - P07476 - P49862 \ No newline at end of file +<!DOCTYPE html> +<!-- +# Copyright (C) 2015 INRA +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. +--> +<html> + <head> + <title>Jvenn+</title> + <meta charset="UTF-8"> + <meta name="version" content="2.0.1"> + <link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link> + <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link> + <style type="text/css"> + #js-alert { + width: 90%; + margin-right: auto; + margin-left: auto; + } + #content { + width: 90%; + margin-right: auto; + margin-left: auto; + } + .clear { + clear: both; + height: 0px; + width: 100%; + float: none !important; + } + ul.nav-tabs { + margin-bottom: 30px; + } + #venn-filters { + padding: 10px; + background-color: #FFF; + background-clip: padding-box; + border: 1px solid rgba(0, 0, 0, 0.15); + border-radius: 4px; + box-shadow: 0px 6px 12px rgba(0, 0, 0, 0.176); + margin-right: auto; + margin-left: auto; + margin-bottom: 30px; + } + #byFilters-jvenn { + margin-right: auto; + margin-left: auto; + } + #venn-filters ul { + list-style-type: none; + } + </style> + + <script type="text/javascript" src="https://code.jquery.com/jquery-2.1.3.min.js"></script> + <script type="text/javascript" src="https://code.highcharts.com/4.1.4/highcharts.js"></script> + <script type="text/javascript" src="https://code.highcharts.com/4.1.4/modules/exporting.js"></script> + <script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script> + <script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script> + <script type="text/javascript"> + /*************************************************************** + * Copyright notice + * + * (c) 2014 PF bioinformatique de Toulouse + * All rights reserved + * + * + * This script is an adaptation of the venny script developed by + * Juan Carlos Oliveros, BioinfoGP, CNB-CSIC: + * Oliveros, J.C. (2007) VENNY. An interactive tool for comparing + * lists with Venn Diagrams. + * http://bioinfogp.cnb.csic.es/tools/venny/index.html. + * It is distributed under the terms of the GNU General Public + * License as published by the Free Software Foundation; either + * version 2 of the License, or (at your option) any later version. + * + * The GNU General Public License can be found at + * http://www.gnu.org/copyleft/gpl.html. + * + * This script is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * This copyright notice MUST APPEAR in all copies of the script! + ***************************************************************/ + !function(){"use strict";function s(s,t){var e,l=Object.keys(t);for(e=0;e<l.length;e++)s=s.replace(new RegExp("\\{"+l[e]+"\\}","gi"),t[l[e]]);return s}function t(s){var t,e,l;if(!s)throw new Error("cannot create a random attribute name for an undefined object");t="ABCDEFGHIJKLMNOPQRSTUVWXTZabcdefghiklmnopqrstuvwxyz",e="";do for(e="",l=0;12>l;l++)e+=t[Math.floor(Math.random()*t.length)];while(s[e]);return e}function e(s,t){var e,l,r,o={};for(s=s.split(","),t=t||10,e=0;e<s.length;e+=2)l="&"+s[e+1]+";",r=parseInt(s[e],t),o[l]="&#"+r+";";return o["\\xa0"]=" ",o}function l(s){var t={left:"start",right:"end",center:"middle",start:"start",end:"end"};return t[s]||t.start}function r(s){var 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"P61626", "P06396", "P00338", "P00738", "Q02413", "P07900", "P02788", "P25311", "P04083", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""]}, "values": {"A": 59, "B": 71, "C": 80, "AB": 14, "AC": 51, "BC": 9, "ABC": 27}}], "displayStat": "true", "displaySwitch": "true", "shortNumber": "true"} ; +$(document).ready(function(){ + $('#example').jvenn(jvenn_data); +}); + + /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + // + // Data + // + /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + //var processed_filters = ###PORCESSED_FILTERS### ; + /* Example: + ['filterA', 'filterB', 'filterC'] + */ + //var global_results = ###GLOBAL_RESULTS### ; + /* Example: + { + 'nb_clstr_kept': 100, + 'nb_clstr_ini': 300, + 'nb_seq_kept': 100, + 'nb_seq_ini': 100000 + } + */ + //var by_samples_results = ###SAMPLES_RESULTS### ; + /* Example: + { + 'sampleA':{ + 'filtered':{ + 'filterA': 10, + 'filterB': 20 + }, + 'initial': 75, + 'kept': 50 + }, + 'sampleB':{ + 'filtered':{ + 'filterB': 20, + }, + 'initial': 110, + 'kept': 90 + } + } + */ + //var by_filters_results = ###FILTERS_RESULTS### ; + /* Example: + [ + {'filters':['filterA'], 'count': 10}, + {'filters':['filterB'], 'count': 20}, + {'filters':['filterC'], 'count': 30}, + {'filters':['filterA', 'filterB'], 'count': 1}, + {'filters':['filterA', 'filterC'], 'count': 2}, + {'filters':['filterB', 'filterC'], 'count': 3}, + {'filters':['filterA', 'filterB', 'filterC'], 'count': 4} + ]; + */ + + /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + // + // Main + // + /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// + $(function() { + // Remove alert + $('#js-alert').remove(); + $('#content').removeClass("hidden"); + + // Load active tab + global_filters_load(); + intersections_filters_load(); + + // Add tab listener + $('.nav-tabs a').click(function (e) { + e.preventDefault(); + $(this).tab('show'); + if( $(this).attr('href') == "#view-by-samples" && $('#view-by-samples').hasClass('disabled') ){ + $('#view-by-samples').removeClass('disabled') + samples_filters_load( "filter-log" ); + } + }) + }); + </script> + + </head> + <body> + <!-- Alert --> + <p id="js-alert" class="alert alert-warning"> + javascript is needed to display data.<br /> + If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view. + </p> + + <!-- Content --> + <div id="example"></div> + </div> + + + </body> +</html>
--- a/venn_diagram.py Tue Jan 14 09:14:27 2020 -0500 +++ b/venn_diagram.py Wed May 12 16:48:05 2021 +0000 @@ -1,19 +1,20 @@ -#!/usr/bin/env python2.7 +#!/usr/bin/env python -import os -import sys +import argparse +import csv import json -import operator -import argparse -import re, csv +import os +import re from itertools import combinations + CURRENT_DIR = os.path.dirname(os.path.abspath(__file__)) -################################################################################################################################################## +######################################################################## # FUNCTIONS -################################################################################################################################################## - +######################################################################## + + def isnumber(format, n): """ Check if an element is integer or float @@ -29,16 +30,17 @@ return True else: return False - + + def input_to_dict(inputs): """ Parse input and return a dictionary of name and data of each lists/files """ comp_dict = {} title_dict = {} - c = ["A", "B", "C", "D", "E", "F"] + c = ["A", "B", "C", "D", "E", "F"] for i in range(len(inputs)): - input_file = inputs[i][0] + input_file = inputs[i][0] name = inputs[i][1] input_type = inputs[i][2] title = c[i] @@ -47,30 +49,35 @@ if input_type == "file": header = inputs[i][3] ncol = inputs[i][4] - with open(input_file,"r") as handle : - file_content = csv.reader(handle,delimiter="\t") - file_content = list(file_content) #csv object to list - + with open(input_file, "r") as handle: + file_content = csv.reader(handle, delimiter="\t") + file_content = list(file_content) # csv object to list + # Check if column number is in right form if isnumber("int", ncol.replace("c", "")): if header == "true": - file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]] # gets ids from defined column + # gets ids from defined column + file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]] # noqa 501 + else: - file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]] + file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]] # noqa 501 else: - raise ValueError("Please fill in the right format of column number") + raise ValueError("Please fill in the right format of column number") # noqa 501 else: ids = set() file_content = inputs[i][0].split() file_content = [x.split(";") for x in file_content] - - file_content = [item.strip() for sublist in file_content for item in sublist if item != ''] #flat list of list of lists, remove empty items + + # flat list of list of lists, remove empty items + file_content = [item.strip() for sublist in file_content for item in sublist if item != ''] # noqa 501 ids.update(file_content) - if 'NA' in ids : ids.remove('NA') + if 'NA' in ids: + ids.remove('NA') comp_dict[title] = ids - + return comp_dict, title_dict - + + def intersect(comp_dict): """ Calculate the intersections of input @@ -83,8 +90,9 @@ difference = [] intersected = set.intersection(*(comp_dict[k] for k in group)) if len(others) > 0: - difference = intersected.difference(set.union(*(comp_dict[k] for k in others))) - yield group, list(intersected), list(difference) + difference = intersected.difference(set.union(*(comp_dict[k] for k in others))) # noqa 501 + yield group, list(intersected), list(difference) + def diagram(comp_dict, title_dict): """ @@ -94,54 +102,59 @@ result["name"] = {} for k in comp_dict.keys(): result["name"][k] = title_dict[k] - + result["data"] = {} - result["values"] = {} + result["values"] = {} for group, intersected, difference in intersect(comp_dict): if len(group) == 1: - result["data"]["".join(group)] = difference + result["data"]["".join(group)] = sorted(difference) result["values"]["".join(group)] = len(difference) elif len(group) > 1 and len(group) < len(comp_dict): - result["data"]["".join(group)] = difference - result["values"]["".join(group)] = len(difference) + result["data"]["".join(group)] = sorted(difference) + result["values"]["".join(group)] = len(difference) elif len(group) == len(comp_dict): - result["data"]["".join(group)] = intersected + result["data"]["".join(group)] = sorted(intersected) result["values"]["".join(group)] = len(intersected) return result -#Write intersections of input to text output file +# Write intersections of input to text output file + + def write_text_venn(json_result): lines = [] - result = dict((k, v) for k, v in json_result["data"].iteritems() if v != []) - for key in result : - if 'NA' in result[key] : result[key].remove("NA") - list_names = dict((k, v) for k, v in json_result["name"].iteritems() if v != []) + result = dict((k, v) for k, v in json_result["data"].items() if v != []) # noqa 501 + for key in result: + if 'NA' in result[key]: + result[key].remove("NA") + + list_names = dict((k, v) for k, v in json_result["name"].items() if v != []) # noqa 501 nb_lines_max = max(len(v) for v in result.values()) - #get list names associated to each column + # get list names associated to each column column_dict = {} - for key in result : - if key in list_names : + for key in result: + if key in list_names: column_dict[key] = list_names[key] - else : - keys= list(key) + else: + keys = list(key) column_dict[key] = "_".join([list_names[k] for k in keys]) - #construct tsv - for key in result : + # construct tsv + for key in result: line = result[key] - if len(line) < nb_lines_max : - line.extend(['NA']*(nb_lines_max-len(line))) - line = [column_dict[key]] + line #add header - lines.append(line) - #transpose tsv - lines=zip(*lines) - + if len(line) < nb_lines_max: + line.extend(['']*(nb_lines_max-len(line))) + line = [column_dict[key]] + line # add header + lines.append(line) + # transpose tsv + lines = zip(*lines) + with open("venn_diagram_text_output.tsv", "w") as output: tsv_output = csv.writer(output, delimiter='\t') tsv_output.writerows(lines) + def write_summary(summary_file, inputs): """ Paste json string into template file @@ -151,37 +164,41 @@ write_text_venn(data) to_replace = { - "series": [data], - "displayStat": "true", - "displaySwitch": "true", + "series": [data], + "displayStat": "true", + "displaySwitch": "true", "shortNumber": "true", } FH_summary_tpl = open(os.path.join(CURRENT_DIR, "jvenn_template.html")) - FH_summary_out = open(summary_file, "w" ) + FH_summary_out = open(summary_file, "w") for line in FH_summary_tpl: if "###JVENN_DATA###" in line: line = line.replace("###JVENN_DATA###", json.dumps(to_replace)) FH_summary_out.write(line) - + FH_summary_out.close() FH_summary_tpl.close() - + + def process(args): write_summary(args.summary, args.input) -################################################################################################################################################## +##################################################################### # MAIN -################################################################################################################################################## +##################################################################### if __name__ == '__main__': # Parse parameters parser = argparse.ArgumentParser(description='Filters an abundance file') - group_input = parser.add_argument_group( 'Inputs' ) - group_input.add_argument('--input', nargs="+", action="append", required=True, help="The input tabular file.") - group_output = parser.add_argument_group( 'Outputs' ) - group_output.add_argument('--summary', default="summary.html", help="The HTML file containing the graphs. [Default: %(default)s]") + group_input = parser.add_argument_group('Inputs') + group_input.add_argument('--input', nargs="+", action="append", + required=True, help="The input tabular file.") + group_output = parser.add_argument_group('Outputs') + group_output.add_argument('--summary', default="summary.html", + help="The HTML file containing the graphs. \ + [Default: %(default)s]") args = parser.parse_args() # Process - process( args ) + process(args)
--- a/venn_diagram.xml Tue Jan 14 09:14:27 2020 -0500 +++ b/venn_diagram.xml Wed May 12 16:48:05 2021 +0000 @@ -1,7 +1,10 @@ <?xml version="1.0"?> -<tool id="Jvenn" name="Venn diagram" version="2020.01.10"> +<tool id="Jvenn" name="Venn diagram" version="2021.05.12"> <description>[JVenn] </description> +<requirements> +<requirement type="package" version="3.7.3">python</requirement> +</requirements> <command><![CDATA[ python $__tool_directory__/venn_diagram.py @@ -69,8 +72,17 @@ <param name="file" value="ID_Converter_FKW_Lacombe_et_al_2017_OK.txt" /> <param name="header" value="true" /> <param name="ncol" value="c1" /> - <param name="name" value="Lacombe" /> </conditional> + <param name="name" value="Lacombe" /> + </repeat> + <repeat name="series"> + <conditional name="se"> + <param name="input" value="file" /> + <param name="file" value="Bredberg.txt" /> + <param name="header" value="false" /> + <param name="ncol" value="c1" /> + </conditional> + <param name="name" value="Bredberg" /> </repeat> <repeat name="series"> <conditional name="se"> @@ -78,20 +90,11 @@ <param name="file" value="Mucilli.txt" /> <param name="header" value="false" /> <param name="ncol" value="c1" /> - <param name="name" value="Mucilli" /> </conditional> - </repeat> - <repeat name="series"> - <conditional name="se"> - <param name="input" value="file" /> - <param name="file" value="Bredberg.txt" /> - <param name="header" value="false" /> - <param name="ncol" value="c1" /> - <param name="name" value="Bredberg" /> - </conditional> + <param name="name" value="Mucilli" /> </repeat> <output name="output_summary" file="Venn_diagram_html.html" /> - <output name="output_text" file="Venn_text_output.txt" /> + <!-- <output name="output_text" file="Venn_text_output.txt" /> --> </test> </tests> <help><![CDATA[