| Previous changeset 10:e744a43171ff (2020-01-14) |
|
Commit message:
"planemo upload commit 00cab92333b0338cb86ff78b5bbc1b6d26621012-dirty" |
|
modified:
test-data/Venn_diagram_html.html test-data/Venn_text_output.txt venn_diagram.py venn_diagram.xml |
| b |
| diff -r e744a43171ff -r 958eb2ea02aa test-data/Venn_diagram_html.html --- 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 |
| [ |
| b'@@ -62,9 +62,9 @@\n \t\t\t}\n \t\t</style>\n \n-\t\t<script type="text/javascript" src="http://code.jquery.com/jquery-2.1.3.min.js"></script>\n-\t\t<script type="text/javascript" src="http://code.highcharts.com/4.1.4/highcharts.js"></script>\n-\t\t<script type="text/javascript" src="http://code.highcharts.com/4.1.4/modules/exporting.js"></script>\n+\t\t<script type="text/javascript" src="https://code.jquery.com/jquery-2.1.3.min.js"></script>\n+\t\t<script type="text/javascript" src="https://code.highcharts.com/4.1.4/highcharts.js"></script>\n+\t\t<script type="text/javascript" src="https://code.highcharts.com/4.1.4/modules/exporting.js"></script>\n \t\t<script type="text/javascript" src="https://cdn.datatables.net/1.10.6/js/jquery.dataTables.min.js"></script>\n \t\t<script type="text/javascript" src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>\n \t\t<script type="text/javascript">\n@@ -95,8 +95,8 @@\n \t\t\t* This copyright notice MUST APPEAR in all copies of the script!\n \t\t\t***************************************************************/\n \t\t\t!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 t={alphabetic:"alphabetic",hanging:"hanging",top:"text-before-edge",bottom:"text-after-edge",middle:"central"};return t[s]||t.alphabetic}var 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"P01613", "P01617", "P01621", "P01622", "P01714", "P01717", "P01880", "P02647", "P02649", "P02747", "P02751", "P02760", "P02766", "P02774", "P02790", "P04117", "P04196", "P04217", "P04233", "P04637", "P05155", "P05362", "P06313", "P06681", "P08238", "P08758", "P0C0L4", "P0C0L5", "P10909", "P11217", "P11686", "P12429", "P15814", "P19827", "P22897", "P23528", "P43652", "P61769", "P62807", "P80748", "Q08380", "Q13885", "Q14624", "Q16378", "Q6MZX7", "Q6N093", "Q7Z351", "Q86SJ6", "Q8IWL2", "Q8NF17", "Q96S96", "Q9BYE4", "Q9NSK0", "Q9UBC9", "Q9UL77", "Q9UL83", "Q9UL86", "", "", "", "", "", "", "", "", ""], "C": ["O15523", "O43175", "O43790", "O60814", "P01593", "P01620", "P01861", "P02533", "P02671", "P02675", "P02679", "P03973", "P04264", "P05091", "P05120", "P05783", "P06576", "P06702", "P07476", "P08107", "P0CG48", "P10809", "P12035", "P13489", "P13645", "P13647", "P14174", "P15880", "P17900", "P17931", "P22392", "P22531", "P22735", "P23490", "P23526", "P25787", "P28070", "P28072", 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"P08865", "P09211", "P11021", "P11142", "P13639", "P13646", "P14618", "P14735", "P14923", "P18206", "P19013", "P20933", "P26641", "P29508", "P31944", "P31949", "P36952", "P40926", "P47756", "P47929", "P58107", "P60174", "P60842", "P68371", "Q04695", "Q06830", "Q5T750", "Q6KB66", "Q6UWP8", "Q8N1N4", "Q8WVV4", "Q9C075", "Q9NZH8", "Q9NZT1", "Q9UIV8", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], "BC": ["P01023", "P05109", "P07737", "P59665", "P60709", "P62805", "Q13835", "Q15517", "Q5D862", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], "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"} ;\n $(document).ready(function(){\n $(\'#example\').jvenn(jvenn_data);\n });\n@@ -152,7 +152,7 @@\n \t\t\t\t\t\'nb_seq_ini\': 100000\n \t\t\t\t}\n \t\t\t*/\n-\t\t\t//var by_samples_results =\xc2\xa0###SAMPLES_RESULTS### ;\n+\t\t\t//var by_samples_results = ###SAMPLES_RESULTS### ;\n \t\t\t/* Example:\n \t\t\t\t{\n \t\t\t\t\t\'sampleA\':{\n@@ -172,7 +172,7 @@\n \t\t\t\t\t}\n \t\t\t\t}\n \t\t\t*/\n-\t\t\t//var by_filters_results =\xc2\xa0###FILTERS_RESULTS### ;\n+\t\t\t//var by_filters_results = ###FILTERS_RESULTS### ;\n \t\t\t/* Example:\n \t\t\t\t[\n \t\t\t\t\t{\'filters\':[\'filterA\'], \'count\': 10},\n' |
| b |
| diff -r e744a43171ff -r 958eb2ea02aa test-data/Venn_text_output.txt --- 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 |
| [ |
| b'@@ -1,81 +1,228 @@\n-Lacombe\tBredberg\tMucilli\tMucilli_Bredberg\tLacombe_Bredberg\tLacombe_Mucilli_Bredberg\tLacombe_Mucilli\t\n-P0DMV9\tP04217\tQ7Z794\tQ13835\tP02787\tP02768\tP08779\t\n-Q9Y6R7\tP02649\tP51149\tP01023\tP01833\tP10599\tP04259\t\n-P30740\tQ7Z351\tP17900\tP59665\tP01625\tP07355\tO75223\t\n-P68363\tP08758\tQ96KK5\tQ15517\tP22528\tQ01469\tP47756\t\n-O75635\tQ9UBC9\tP10809\tP05109\tQ9UGM3\tP68871\tP06733\t\n-O60911\tP02760\tO43175\tP60709\tQ96DA0\tP07900\tP20933\t\n-P61160\tO95436\tQ6ZVX7\tP62805\tP02763\tP15924\tQ9NZH8\t\n-Q15828\tP02647\tP01861\tQ5D862\tP61916\tP25311\tP09211\t\n-P23284\tP15814\tP14174\tP07737\tP01009\tQ86YZ3\tP04792\t\n-P20930\tQ9NSK0\tP01593\t\tP12273\tP05089\tP36952\t\n-P01860\tP01717\tQ15365\t\tQ13867\tQ08188\tP01040\t\n-Q96FX8\tP04117\tP37802\t\tP01765\tP04406\tP60174\t\n-P62937\tQ13885\tP29373\t\tP01036\tP07339\tP26641\t\n-Q15149\tP01591\tP30050\t\tP01011\tP06396\tP14618\t\n-P25705\tO95613\tQ6E0U4\t\t\tP00338\tP31944\t\n-P19971\tP01880\tP23526\t\t\tP61626\tQ8N1N4\t\n-O75342\tP04233\tQ13748\t\t\tP04083\tP04075\t\n-Q92820\tP01598\tP05120\t\t\tQ02413\tP14923\t\n-P25788\tP01621\tQ14134\t\t\tP27482\tQ8WVV4\t\n-Q9HCY8\tQ9UL77\tP68431\t\t\tP01871\tO75369\t\n-P19012\tP05362\tP35527\t\t\tP80188\tP00558\t\n-Q8TAX7\tP01024\tQ5XKE5\t\t\tP31947\tP19013\t\n-P42357\tQ86SJ6\tO15523\t\t\tP31025\tQ5T750\t\n-P50395\tP12429\tP25787\t\t\tQ96P63\tP14735\t\n-P01766\tP43652\tP22392\t\t\tP63104\tP47929\t\n-P40121\tP22897\tP49189\t\t\tP00738\tQ06830\t\n-P04080\tP06313\tP61978\t\t\tP02788\tP29508\t\n-Q9HC84\tB4E1Z4\tP32119\t\t\t\tP68371\t\n-P59998\tP01008\tQ5VVQ6\t\t\t\tQ9NZT1\t\n-P23396\tA2IPI6\tQ8IW75\t\t\t\tP11142\t\n-P00491\tP02790\tP01620\t\t\t\tP40926\t\n-P62258\tP61769\tP02671\t\t\t\tP01876\t\n-P01623\tP00450\tP62244\t\t\t\tP58107\t\n-P31151\tQ08380\tP0CG48\t\t\t\tP01834\t\n-Q6P4A8\tP02751\tP02675\t\t\t\tP18206\t\n-P63261\tQ8NF17\tQ9Y277\t\t\t\tQ04695\t\n-P01877\tQ14624\tP02679\t\t\t\tP08865\t\n-P09228\tP0C0L5\tP02533\t\t\t\tP13646\t\n-P48637\tP0C0L4\tQ9Y337\t\t\t\tP02545\t\n-P07858\tQ9UL83\tP12035\t\t\t\tP04040\t\n-P07384\tP08238\tP52907\t\t\t\tP13639\t\n-P06870\tP02766\tP35321\t\t\t\tP05090\t\n-Q9UI42\tQ9UL86\tP13489\t\t\t\tQ6KB66\t\n-P35579\tP02774\tP29401\t\t\t\tP01857\t\n-P13473\tP05155\tP04264\t\t\t\tQ6UWP8\t\n-P62987\tP11686\tQ14210\t\t\t\tQ9UIV8\t\n-P04745\tP01622\tP28074\t\t\t\tQ9C075\t\n-P49720\tQ6N093\tP40925\t\t\t\tO43707\t\n-P11279\tP04637\tP28070\t\t\t\tP11021\t\n-P18510\tQ96S96\tP28072\t\t\t\tP31949\t\n-Q14574\tP62807\tQ14CN4\t\t\t\tP60842\t\n-P02538\tP23528\tQ9Y3R4\t\t\t\t\t\n-P48594\tP10909\tP13647\t\t\t\t\t\n-A8K2U0\tA4F255\tP54652\t\t\t\t\t\n-P09972\tP00734\tQ08554\t\t\t\t\t\n-O95274\tP19827\tP08107\t\t\t\t\t\n-P01037\tQ16378\tP30041\t\t\t\t\t\n-P0CG05\tP01714\tP06702\t\t\t\t\t\n-P00441\tP11217\tO43790\t\t\t\t\t\n-\tA0A0U1RVJ5\tQ96QA5\t\t\t\t\t\n-\tP01617\tP23490\t\t\t\t\t\n-\tP01611\tP22735\t\t\t\t\t\n-\tP04196\tP13645\t\t\t\t\t\n-\tP01613\tP17931\t\t\t\t\t\n-\tP02747\tQ3ZCW2\t\t\t\t\t\n-\tP80748\tP68104\t\t\t\t\t\n-\tA0N5G5\tP06576\t\t\t\t\t\n-\tQ8IWL2\tQ5T749\t\t\t\t\t\n-\tQ9BYE4\tP05091\t\t\t\t\t\n-\tP06681\tO60814\t\t\t\t\t\n-\tQ6MZX7\tP37837\t\t\t\t\t\n-\t\tP22531\t\t\t\t\t\n-\t\tP03973\t\t\t\t\t\n-\t\tP63167\t\t\t\t\t\n-\t\tP05783\t\t\t\t\t\n-\t\tP50990\t\t\t\t\t\n-\t\tP15880\t\t\t\t\t\n-\t\tP35908\t\t\t\t\t\n-\t\tP07476\t\t\t\t\t\n-\t\tP49862\t\t\t\t\t\n\\ No newline at end of file\n+<!DOCTYPE html>\n+<!--\n+# Copyright (C) 2015 INRA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program. If not, see <http://www.gnu.org/licenses/>.\n+-->\n+<html>\n+\t<head>\n+\t\t<title>Jvenn+</title>\n+\t\t<meta charset="UTF-8">\n+\t\t<meta name="version" content="2.0.1">\n+\t\t<link rel="stylesheet" href="https://cdn.datatables.net/1.10.6/css/jquery.dataTables.css"></link>\n+\t\t<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"></link>\n+\t\t<style type="text/css">\n+\t\t\t#js-alert {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t#content {\n+\t\t\t\twidth: 90%;\n+\t\t\t\tmargin-right: auto;\n+\t\t\t\tmargin-left: auto;\n+\t\t\t}\n+\t\t\t.clear {\n+\t\t\t\tclear: both;\n+\t'..b'4259", "P68371", "Q9NZH8", "P26641", "P13646", "P02545", "Q8N1N4", "Q06830", "P01834", "O43707", "P47929", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], "BC": ["P07737", "P60709", "Q5D862", "Q15517", "Q13835", "P05109", "P62805", "P01023", "P59665", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], "ABC": ["Q96P63", "P80188", "P10599", "P01871", "P31025", "Q86YZ3", "P27482", "P02768", "P07355", "P63104", "P04406", "P15924", "Q08188", "P07339", "P05089", "Q01469", "P31947", "P68871", "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"} ;\n+$(document).ready(function(){\n+ $(\'#example\').jvenn(jvenn_data);\n+});\n+\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Data\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//var processed_filters = ###PORCESSED_FILTERS### ;\n+\t\t\t/* Example:\n+\t\t\t\t[\'filterA\', \'filterB\', \'filterC\']\n+\t\t\t*/\n+\t\t\t//var global_results = ###GLOBAL_RESULTS### ; \n+\t\t\t/* Example: \n+\t\t\t\t{\n+\t\t\t\t\t\'nb_clstr_kept\': 100,\n+\t\t\t\t\t\'nb_clstr_ini\': 300,\n+\t\t\t\t\t\'nb_seq_kept\': 100,\n+\t\t\t\t\t\'nb_seq_ini\': 100000\n+\t\t\t\t}\n+\t\t\t*/\n+\t\t\t//var by_samples_results = ###SAMPLES_RESULTS### ;\n+\t\t\t/* Example:\n+\t\t\t\t{\n+\t\t\t\t\t\'sampleA\':{\n+\t\t\t\t\t\t\'filtered\':{\n+\t\t\t\t\t\t\t\'filterA\': 10,\n+\t\t\t\t\t\t\t\'filterB\': 20\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\t\'initial\': 75,\n+\t\t\t\t\t\t\'kept\': 50\n+\t\t\t\t\t},\n+\t\t\t\t\t\'sampleB\':{\n+\t\t\t\t\t\t\'filtered\':{\n+\t\t\t\t\t\t\t\'filterB\': 20,\n+\t\t\t\t\t\t},\n+\t\t\t\t\t\t\'initial\': 110,\n+\t\t\t\t\t\t\'kept\': 90\n+\t\t\t\t\t}\n+\t\t\t\t}\n+\t\t\t*/\n+\t\t\t//var by_filters_results = ###FILTERS_RESULTS### ;\n+\t\t\t/* Example:\n+\t\t\t\t[\n+\t\t\t\t\t{\'filters\':[\'filterA\'], \'count\': 10},\n+\t\t\t\t\t{\'filters\':[\'filterB\'], \'count\': 20},\n+\t\t\t\t\t{\'filters\':[\'filterC\'], \'count\': 30},\n+\t\t\t\t\t{\'filters\':[\'filterA\', \'filterB\'], \'count\': 1},\n+\t\t\t\t\t{\'filters\':[\'filterA\', \'filterC\'], \'count\': 2},\n+\t\t\t\t\t{\'filters\':[\'filterB\', \'filterC\'], \'count\': 3},\n+\t\t\t\t\t{\'filters\':[\'filterA\', \'filterB\', \'filterC\'], \'count\': 4}\n+\t\t\t\t];\n+\t\t\t*/\n+\t\t\t\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t//\n+\t\t\t// Main\n+\t\t\t//\n+\t\t\t///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////\n+\t\t\t$(function() {\n+\t\t\t\t// Remove alert\n+\t\t\t\t$(\'#js-alert\').remove();\n+\t\t\t\t$(\'#content\').removeClass("hidden");\n+\t\t\t\t\n+\t\t\t\t// Load active tab\n+\t\t\t\tglobal_filters_load();\n+\t\t\t\tintersections_filters_load();\n+\t\t\t\t\n+\t\t\t\t// Add tab listener\n+\t\t\t\t$(\'.nav-tabs a\').click(function (e) {\n+\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t$(this).tab(\'show\');\n+\t\t\t\t\tif( $(this).attr(\'href\') == "#view-by-samples" && $(\'#view-by-samples\').hasClass(\'disabled\') ){\n+\t\t\t\t\t\t$(\'#view-by-samples\').removeClass(\'disabled\')\n+\t\t\t\t\t\tsamples_filters_load( "filter-log" );\n+\t\t\t\t\t}\n+\t\t\t\t})\n+\t\t\t});\n+\t\t</script>\n+\n+\t</head>\n+\t<body>\n+\t\t<!-- Alert -->\n+\t\t<p id="js-alert" class="alert alert-warning">\n+ javascript is needed to display data.<br />\n+ If you try to view this data on galaxy please contact your administrator to authorise javascript or download the file to view.\n+\t\t</p>\n+\t\t\n+ <!-- Content -->\n+\t<div id="example"></div>\n+ </div>\n+\n+\t\t\n+\t</body>\n+</html>\n' |
| b |
| diff -r e744a43171ff -r 958eb2ea02aa venn_diagram.py --- a/venn_diagram.py Tue Jan 14 09:14:27 2020 -0500 +++ b/venn_diagram.py Wed May 12 16:48:05 2021 +0000 |
| [ |
| b'@@ -1,19 +1,20 @@\n-#!/usr/bin/env python2.7\n+#!/usr/bin/env python\n \n-import os\n-import sys\n+import argparse\n+import csv\n import json\n-import operator\n-import argparse\n-import re, csv\n+import os\n+import re\n from itertools import combinations\n \n+\n CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))\n \n-##################################################################################################################################################\n+########################################################################\n # FUNCTIONS\n-##################################################################################################################################################\n- \n+########################################################################\n+\n+\n def isnumber(format, n):\n """\n Check if an element is integer or float\n@@ -29,16 +30,17 @@\n return True\n else:\n return False\n- \n+\n+\n def input_to_dict(inputs):\n """\n Parse input and return a dictionary of name and data of each lists/files\n """\n comp_dict = {}\n title_dict = {}\n- c = ["A", "B", "C", "D", "E", "F"] \n+ c = ["A", "B", "C", "D", "E", "F"]\n for i in range(len(inputs)):\n- input_file = inputs[i][0] \n+ input_file = inputs[i][0]\n name = inputs[i][1]\n input_type = inputs[i][2]\n title = c[i]\n@@ -47,30 +49,35 @@\n if input_type == "file":\n header = inputs[i][3]\n ncol = inputs[i][4]\n- with open(input_file,"r") as handle :\n- file_content = csv.reader(handle,delimiter="\\t")\n- file_content = list(file_content) #csv object to list\n- \n+ with open(input_file, "r") as handle:\n+ file_content = csv.reader(handle, delimiter="\\t")\n+ file_content = list(file_content) # csv object to list\n+\n # Check if column number is in right form\n if isnumber("int", ncol.replace("c", "")):\n if header == "true":\n- file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]] # gets ids from defined column\n+ # gets ids from defined column\n+ file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]] # noqa 501\n+\n else:\n- file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]] \n+ file_content = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]] # noqa 501\n else:\n- raise ValueError("Please fill in the right format of column number") \n+ raise ValueError("Please fill in the right format of column number") # noqa 501\n else:\n ids = set()\n file_content = inputs[i][0].split()\n file_content = [x.split(";") for x in file_content]\n- \n- file_content = [item.strip() for sublist in file_content for item in sublist if item != \'\'] #flat list of list of lists, remove empty items \n+\n+ # flat list of list of lists, remove empty items\n+ file_content = [item.strip() for sublist in file_content for item in sublist if item != \'\'] # noqa 501\n ids.update(file_content)\n- if \'NA\' in ids : ids.remove(\'NA\')\n+ if \'NA\' in ids:\n+ ids.remove(\'NA\')\n comp_dict[title] = ids\n- \n+\n return comp_dict, title_dict\n- \n+\n+\n def intersect(comp_dict):\n """\n Calculate the intersections of input\n@@ -83,8 +90,9 @@\n difference = []\n intersected = set.intersection(*(comp_dict[k] for k in group))\n if len(others) > 0:\n- difference = intersected.difference(set.union(*(comp_dict[k] for k in others)))\n- y'..b'\n- list_names = dict((k, v) for k, v in json_result["name"].iteritems() if v != [])\n+ result = dict((k, v) for k, v in json_result["data"].items() if v != []) # noqa 501\n+ for key in result:\n+ if \'NA\' in result[key]:\n+ result[key].remove("NA")\n+\n+ list_names = dict((k, v) for k, v in json_result["name"].items() if v != []) # noqa 501\n nb_lines_max = max(len(v) for v in result.values())\n \n- #get list names associated to each column\n+ # get list names associated to each column\n column_dict = {}\n- for key in result :\n- if key in list_names :\n+ for key in result:\n+ if key in list_names:\n column_dict[key] = list_names[key]\n- else : \n- keys= list(key)\n+ else:\n+ keys = list(key)\n column_dict[key] = "_".join([list_names[k] for k in keys])\n \n- #construct tsv\n- for key in result :\n+ # construct tsv\n+ for key in result:\n line = result[key]\n- if len(line) < nb_lines_max :\n- line.extend([\'NA\']*(nb_lines_max-len(line)))\n- line = [column_dict[key]] + line #add header\n- lines.append(line) \n- #transpose tsv\n- lines=zip(*lines)\n- \n+ if len(line) < nb_lines_max:\n+ line.extend([\'\']*(nb_lines_max-len(line)))\n+ line = [column_dict[key]] + line # add header\n+ lines.append(line)\n+ # transpose tsv\n+ lines = zip(*lines)\n+\n with open("venn_diagram_text_output.tsv", "w") as output:\n tsv_output = csv.writer(output, delimiter=\'\\t\')\n tsv_output.writerows(lines)\n \n+\n def write_summary(summary_file, inputs):\n """\n Paste json string into template file\n@@ -151,37 +164,41 @@\n write_text_venn(data)\n \n to_replace = {\n- \t"series": [data],\n- \t"displayStat": "true",\n- \t"displaySwitch": "true",\n+ "series": [data],\n+ "displayStat": "true",\n+ "displaySwitch": "true",\n "shortNumber": "true",\n }\n \n FH_summary_tpl = open(os.path.join(CURRENT_DIR, "jvenn_template.html"))\n- FH_summary_out = open(summary_file, "w" )\n+ FH_summary_out = open(summary_file, "w")\n for line in FH_summary_tpl:\n if "###JVENN_DATA###" in line:\n line = line.replace("###JVENN_DATA###", json.dumps(to_replace))\n FH_summary_out.write(line)\n- \n+\n FH_summary_out.close()\n FH_summary_tpl.close()\n- \n+\n+\n def process(args):\n write_summary(args.summary, args.input)\n \n \n-##################################################################################################################################################\n+#####################################################################\n # MAIN\n-##################################################################################################################################################\n+#####################################################################\n if __name__ == \'__main__\':\n # Parse parameters\n parser = argparse.ArgumentParser(description=\'Filters an abundance file\')\n- group_input = parser.add_argument_group( \'Inputs\' )\n- group_input.add_argument(\'--input\', nargs="+", action="append", required=True, help="The input tabular file.")\n- group_output = parser.add_argument_group( \'Outputs\' )\n- group_output.add_argument(\'--summary\', default="summary.html", help="The HTML file containing the graphs. [Default: %(default)s]")\n+ group_input = parser.add_argument_group(\'Inputs\')\n+ group_input.add_argument(\'--input\', nargs="+", action="append",\n+ required=True, help="The input tabular file.")\n+ group_output = parser.add_argument_group(\'Outputs\')\n+ group_output.add_argument(\'--summary\', default="summary.html",\n+ help="The HTML file containing the graphs. \\\n+ [Default: %(default)s]")\n args = parser.parse_args()\n \n # Process\n- process( args )\n+ process(args)\n' |
| b |
| diff -r e744a43171ff -r 958eb2ea02aa venn_diagram.xml --- 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[ |