Mercurial > repos > lnguyen > venn_diagram_plotter
changeset 0:6f22d2726103 draft default tip
planemo upload
author | lnguyen |
---|---|
date | Fri, 15 Sep 2017 09:32:19 -0400 |
parents | |
children | |
files | jvenn_template.html test-data/DESeq.txt test-data/FQ.txt test-data/RPKM.txt test-data/TC.txt test-data/TMM.txt test-data/UQ.txt test-data/venn_diagram_summary.html test-data/venn_diagram_text_output.txt venn_diagram.py venn_diagram.xml |
diffstat | 11 files changed, 7001 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jvenn_template.html Fri Sep 15 09:32:19 2017 -0400 @@ -0,0 +1,228 @@ +<!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="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://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. 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RPKM.txt Fri Sep 15 09:32:19 2017 -0400 @@ -0,0 +1,417 @@ +G000005 +G000008 +G000009 +G000012 +G000028 +G000029 +G000030 +G000061 +G000101 +G000147 +G000165 +G000177 +G000185 +G000195 +G000237 +G000259 +G000262 +G000302 +G000305 +G000306 +G000311 +G000316 +G000355 +G000356 +G000370 +G000376 +G000377 +G000381 +G000412 +G000418 +G000420 +G000426 +G000447 +G000490 +G000514 +G000517 +G000547 +G000581 +G000665 +G000696 +G000701 +G000704 +G000705 +G000711 +G000714 +G000715 +G000717 +G000720 +G000721 +G000722 +G000725 +G000726 +G000728 +G000749 +G000783 +G000824 +G000851 +G000857 +G000899 +G000902 +G000934 +G000951 +G000962 +G000966 +G000984 +G000985 +G000987 +G001006 +G001007 +G001029 +G001043 +G001045 +G001051 +G001053 +G001061 +G001093 +G001102 +G001105 +G001107 +G001112 +G001115 +G001123 +G001136 +G001171 +G001189 +G001218 +G001226 +G001247 +G001283 +G001287 +G001288 +G001317 +G001319 +G001328 +G001343 +G001351 +G001352 +G001359 +G001360 +G001362 +G001386 +G001409 +G001431 +G001461 +G001467 +G001507 +G001525 +G001539 +G001547 +G001554 +G001560 +G001565 +G001575 +G001598 +G001605 +G001620 +G001623 +G001630 +G001633 +G001640 +G001649 +G001650 +G001651 +G001703 +G001704 +G001725 +G001729 +G001736 +G001748 +G001751 +G001753 +G001760 +G001765 +G001771 +G001772 +G001780 +G001791 +G001819 +G001820 +G001840 +G001880 +G001889 +G001890 +G001891 +G001899 +G001904 +G001926 +G001951 +G001975 +G001976 +G001983 +G001987 +G001993 +G001995 +G001998 +G002001 +G002011 +G002024 +G002044 +G002048 +G002050 +G002053 +G002054 +G002055 +G002077 +G002097 +G002101 +G002153 +G002180 +G002199 +G002202 +G002231 +G002254 +G002267 +G002282 +G002297 +G002309 +G002331 +G002332 +G002333 +G002346 +G002361 +G002368 +G002369 +G002373 +G002383 +G002384 +G002385 +G002416 +G002453 +G002462 +G002475 +G002488 +G002497 +G002518 +G002533 +G002551 +G002566 +G002569 +G002594 +G002595 +G002601 +G002610 +G002616 +G002626 +G002628 +G002641 +G002648 +G002658 +G002682 +G002691 +G002693 +G002702 +G002709 +G002710 +G002711 +G002722 +G002755 +G002779 +G002784 +G002797 +G002833 +G002834 +G002885 +G002894 +G002896 +G002899 +G002902 +G002928 +G002953 +G002967 +G002968 +G002969 +G002972 +G002975 +G002981 +G002992 +G002998 +G003023 +G003041 +G003059 +G003075 +G003080 +G003082 +G003093 +G003113 +G003125 +G003142 +G003154 +G003173 +G003177 +G003208 +G003220 +G003222 +G003229 +G003230 +G003304 +G003305 +G003315 +G003317 +G003322 +G003366 +G003388 +G003403 +G003464 +G003486 +G003502 +G003511 +G003539 +G003543 +G003550 +G003558 +G003579 +G003589 +G003592 +G003593 +G003594 +G003602 +G003611 +G003619 +G003628 +G003634 +G003645 +G003747 +G003828 +G003843 +G003847 +G003865 +G003881 +G003901 +G003902 +G003905 +G003912 +G003919 +G003948 +G003962 +G003964 +G004004 +G004034 +G004051 +G004064 +G004095 +G004096 +G004099 +G004113 +G004119 +G004131 +G004136 +G004160 +G004161 +G004170 +G004187 +G004192 +G004210 +G004239 +G004241 +G004258 +G004260 +G004273 +G004293 +G004299 +G004307 +G004324 +G004329 +G004330 +G004349 +G004351 +G004353 +G004373 +G004391 +G004428 +G004466 +G004468 +G004469 +G004471 +G004475 +G004477 +G004479 +G004487 +G004532 +G004543 +G004545 +G004558 +G004565 +G004577 +G004578 +G004589 +G004612 +G004618 +G004623 +G004649 +G004671 +G004712 +G004713 +G004714 +G004715 +G004718 +G004735 +G004762 +G004768 +G004772 +G004783 +G004789 +G004793 +G004856 +G004887 +G004895 +G004907 +G004922 +G004925 +G004932 +G004934 +G004967 +G004992 +G005019 +G005024 +G005043 +G005055 +G005089 +G005094 +G005095 +G005105 +G005119 +G005126 +G005131 +G005154 +G005159 +G005167 +G005169 +G005175 +G005176 +G005180 +G005185 +G005188 +G005192 +G005198 +G005201 +G005202 +G005203 +G005212 +G005214 +G005222 +G005241 +G005243 +G005246 +G005248 +G005250 +G005254 +G005255 +G005259 +G005263 +G005264 +G005266 +G005268 +G005269 +G005273 +G005276
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/venn_diagram_summary.html Fri Sep 15 09:32:19 2017 -0400 @@ -0,0 +1,228 @@ +<!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="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://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. 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"G002464", "G002469", "G002749", "G001929", "G005220", "G004088", "G001022", "G001604", "G001355", "G001606", "G001353", "G001210", "G004302", "G000637", "G000635", "G000631", "G000737", "G000827", "G000730", "G002120", "G003025", "G003342", "G002687", "G001289", "G001324", "G001325", "G001281", "G003938", "G004022", "G003931", "G003163", "G001517", "G001457", "G002051", "G003233", "G003791", "G003238", "G003480", "G003337", "G004470", "G004610", "G000358", "G003800", "G004657", "G004874", "G003808", "G000352", "G004625", "G002228", "G001711", "G004784", "G004377", "G004007", "G001179", "G000078", "G000660", "G004392", "G002096", "G004398", "G002093", "G005227", "G002705", "G002251", "G001108", "G000592", "G001756", "G000772", "G001825", "G002891", "G002439", "G002489", "G002484", "G002957", "G003474", "G002388", "G001083", "G001080", "G002555", "G001394", "G002843", "G001952", "G001073", "G001810", "G001812", "G001776", "G002414", "G002417", "G001227", "G001495", "G001559", "G000468", "G000810", "G000709", "G002671", "G003375", "G004435", "G003076", "G003296", "G000253", "G004220", "G000254", "G001424", "G003949", "G002458", "G000929", "G000927", "G001578", "G004137", "G004501", "G003612", "G004245", "G003201", "G003972", "G004989", "G004988", "G004755", "G004040", "G000405", "G005265", "G004044", "G004980", "G004829", "G002213", "G004290", "G003850", "G004346", "G000317", "G001049", "G003701", "G003538", "G000530", "G000534", "G004535", "G002757", "G002459", "G001910", "G002751", "G002758", "G002320", "G000031", "G001032"], "BDEF": ["G004118"], "A": ["G001905", "G000130", "G000349", "G002946", "G004042", "G002598", "G002420", "G002190", "G004395", "G000389", "G001410", "G000053", "G000189", "G001293", "G001291", "G003379", "G002906", "G000222", "G003407", "G003764", "G002974", "G003644", "G002782", "G002172", "G002079", "G003965", "G000773", "G004036", "G001047", "G004140", "G004711", "G000880", "G004716", "G003934", "G003416", "G004838", "G002205", "G002365", "G004085", "G003453", "G003681", "G001788", "G002084", "G001421", "G003174", "G003630", "G002752", "G004453", "G003690", "G004978", "G002192", "G003433", "G003739", "G003598", "G004208", "G003498", "G001071", "G002640", "G004526", "G000200", "G003425", "G003490", "G002287"], "ACEF": [], "C": [], "B": ["G004580", "G001204", "G002864", "G002803", "G003997", "G001436", "G005184", "G003688", "G000569", "G003544", "G001298", "G004121", "G005031", "G001761", "G004037", "G005014", "G001485", "G004679", "G000570", "G000881", "G001563", "G003758", "G001696", "G004115"], "E": [], "D": [], "ABF": ["G000655", "G004703", "G000046"], "F": ["G003283", "G002316", "G000950", "G001094", "G000919", "G003033", "G003401", "G003940", "G003662", "G002781", "G003484", "G001580", "G002176", "G004364", "G005211", "G005018", "G004659", "G004637", "G001481", "G002220", "G000718", "G000731", "G003851", "G001387", "G002455", "G001139", "G003155"], "ABCDE": [], "EF": ["G001936", "G004930", "G004238", "G000875", "G001275", "G002311", "G003088", "G001657", "G003943", "G001072", "G001509", "G002635", "G000309", "G000471", "G004081"], "ABD": [], "CF": [], "CE": [], "CD": [], "ADF": [], "ADE": [], "ABDE": [], "ACDF": [], "BDF": [], "ABDF": [], "ACDEF": ["G005180"], "ABCDEF": ["G001598", "G000305", "G001343", "G000749", "G005089", "G004967", "G003403", "G001725", "G001729", "G001467", "G001461", "G005250", "G000962", "G000966", "G004096", "G001507", "G004466", "G004543", "G004469", "G003080", "G002628", "G002626", "G003322", "G004649", "G004793", "G004260", "G003142", "G003881", "G004034", "G002899", "G005131", "G000061", "G001890", "G001891", "G002361", "G001899", "G002369", "G002368", "G003041", "G002710", "G002711", "G005222", "G000447", "G002969", "G002968", "G002885", "G000783", "G002967", "G000547", "G001093", "G000665", "G004887", "G002569", "G001820", "G004922", "G004925", "G000147", "G001007", "G001751", "G001760", "G001765", "G001547", "G000714", "G000715", "G000717", "G001780", "G000711", "G001623", "G001620", "G004428", "G003366", "G004907", "G003593", "G003592", "G002101", "G003594", "G004192", "G003919", "G004210", "G003912", "G001539", "G001431", "G003589", "G000934", "G003628", "G002616", "G002610", "G003962", "G003747", "G003964", "G004856", "G004671", "G004992", "G005276", "G004772", "G005273", "G002202", "G003828", "G001998", "G001995", "G001993", "G004351", "G004353", "G000985", "G000984", "G000987", "G002416", "G001283", "G001226", "G001051", "G001053", "G002722", "G001904", "G002331", "G002332", "G002333", "G001123", "G005176", "G005175", "G000028", "G000029", "G000185", "G005094", "G005095", "G002533", "G003558", "G003550", "G001753", "G001976", "G001975", "G002385", "G002384", "G002024", "G001791", "G003388", "G004487", "G004468", "G001575", "G004558", "G001218", "G003093", "G002658", "G002153", "G003315", "G003317", "G004329", "G000420", "G004324", "G001409", "G003177", "G004258", "G000012", "G005126", "G002373", "G000381", "G000376", "G000377", "G004735", "G001704", "G001703", "G003511", "G005192", "G000490", "G005198", "G002475", "G004932", "G004934", "G005043", "G002779", "G002594", "G002595", "G000721", "G000720", "G000725", "G000726", "G001630", "G000728", "G002981", "G001633", "G001288", "G002693", "G002691", "G003059", "G002050", "G002053", "G002975", "G002055", "G002054", "G001840", "G003905", "G003901", "G004161", "G004160", "G001328", "G003634", "G000902", "G003229", "G004119", "G002601", "G004113", "G003222", "G005248", "G005241", "G005243", "G001983", "G002231", "G001987", "G003645", "G000237", "G003125", "G005019", "G000514", "G001061", "G001189", "G000165", "G000696", "G002309", "G000195", "G001386", "G000426", "G004064", "G001115", "G005169", "G000581", "G000517", "G001112", "G002497", "G001362", "G001360", "G003464", "G002011", "G003619", "G003543", "G002833", "G002784", "G002834", "G001748", "G001640", "G001560", "G001565", "G003304", "G003305", "G003865", "G002648", "G004578", "G001247", "G002641", "G004589", "G004623", "G000262", "G001649", "G000899", "G005266", "G003948", "G004241", "G004532", "G000008", "G000009", "G000418", "G000412", "G002928", "G002267", "G003843", "G003847", "G002346", "G000302", "G003113", "G000306", "G004330", "G005201", "G005203", "G005202", "G001736", "G003502", "G005188", "G002199", "G005185", "G005055", "G002297", "G000356", "G001926", "G001605", "G001352", "G001351", "G001359", "G002998", "G002992", "G003023", "G002682", "G002902", "G002048", "G002044", "G001287", "G004170", "G003230", "G004577", "G000857", "G000851", "G004479", "G003486", "G004471", "G002972", "G004475", "G004477", "G004718", "G004307", "G000355", "G004712", "G004713", "G004714", "G004715", "G004783", "G004273", "G004373", "G003154", "G004004", "G005024", "G001171", "G000177", "G001880", "G001889", "G002709", "G002254", "G002383", "G002702", "G005254", "G005255", "G005159", "G004099", "G001102", "G005154", "G004095", "G001107", "G001105", "G002894", "G001319", "G002896", "G002488", "G001317", "G002953", "G003902", "G003579", "G002551", "G004895", "G002001", "G001951", "G001819", "G002797", "G001771", "G001772", "G001554", "G000705", "G000704", "G000701", "G000951", "G001650", "G001651", "G002077", "G003075", "G001006", "G000259", "G004187", "G004565", "G004131", "G004136", "G003208", "G003611", "G005119", "G004762", "G005269", "G005268", "G004768", "G005264", "G005263", "G004299", "G002097", "G000311", "G000316", "G004612", "G005212", "G004349", "G004618", "G001136", "G000101", "G001045", "G001043", "G000005", "G003539", "G003220", "G002755", "G002453", "G005105", "G000030", "G002282"], "ABCDF": [], "BCEF": [], "CDE": [], "CDF": [], "CDEF": ["G004293", "G005246"], "ABE": ["G002821", "G004455", "G003971", "G000024", "G004855"], "ABCD": [], "ABCEF": ["G004239", "G003173", "G004545", "G004051", "G002566", "G002518", "G001525", "G000722", "G001029", "G004391", "G000370", "G003082", "G003602", "G002180", "G005167", "G004789", "G000824", "G005259"], "BDE": [], "ACDE": []}, "name": {"A": "DESeq", "C": "RPKM", "B": "FQ", "E": "TMM", "D": "TC", "F": "UQ"}}], "displaySwitch": "true", "shortNumber": "true", "displayStat": "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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/venn_diagram_text_output.txt Fri Sep 15 09:32:19 2017 -0400 @@ -0,0 +1,485 @@ +FQ_UQ FQ_RPKM_TC DESeq_FQ_RPKM_TMM_UQ DESeq_FQ_TMM_UQ FQ DESeq_TMM_UQ UQ FQ_RPKM_TC_TMM_UQ DESeq_TC_TMM_UQ DESeq_FQ_TC_TMM_UQ DESeq DESeq_FQ DESeq_TMM DESeq_FQ_TMM DESeq_FQ_UQ DESeq_UQ FQ_TMM_UQ TMM_UQ DESeq_RPKM_TC_TMM_UQ DESeq_FQ_RPKM_TC_TMM_UQ RPKM_TC_TMM_UQ FQ_TC_TMM_UQ +G004321 G002462 G004239 G001344 G004580 G001195 G003283 G005214 G001285 G001197 G001905 G002826 G000080 G002821 G000655 G001203 G002976 G001936 G005180 G001598 G004293 G004118 +G002493 G003173 G004551 G001204 G000114 G002316 G002062 G001193 G000130 G004420 G004384 G004455 G004703 G004708 G000483 G004930 G000305 G005246 +G001369 G004545 G001597 G002864 G004177 G000950 G001052 G000349 G003424 G002405 G003971 G000046 G003149 G004238 G001343 +G004173 G004051 G000748 G002803 G001510 G001094 G003936 G002946 G000164 G003427 G000024 G002637 G000875 G000749 +G002562 G002566 G000620 G003997 G000742 G000919 G003838 G004042 G001536 G004700 G004855 G001114 G001275 G005089 + G002518 G000628 G001436 G000510 G003033 G004554 G002598 G001779 G002541 G002037 G002311 G004967 + G001525 G000629 G005184 G002339 G003401 G000391 G002420 G003094 G004994 G003088 G003403 + G000722 G001296 G003688 G003039 G003940 G002234 G002190 G001994 G003751 G001657 G001725 + G001029 G003031 G000569 G004026 G003662 G002237 G004395 G004667 G003943 G001729 + G004391 G001726 G003544 G000994 G002781 G001985 G000389 G004089 G001072 G001467 + G000370 G002038 G001298 G005074 G003484 G002131 G001410 G002905 G001509 G001461 + G003082 G002032 G004121 G001180 G001580 G003232 G000053 G002841 G002635 G005250 + G003602 G001687 G005031 G003397 G002176 G002336 G000189 G001451 G000309 G000962 + G002180 G002526 G001761 G002226 G004364 G004206 G001293 G000471 G000966 + G005167 G001465 G004037 G003792 G005211 G003729 G001291 G004081 G004096 + G004789 G004491 G005014 G000197 G005018 G002912 G003379 G001507 + G000824 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/venn_diagram.py Fri Sep 15 09:32:19 2017 -0400 @@ -0,0 +1,182 @@ +#!/usr/bin/env python2.7 + +import os +import sys +import json +import operator +import argparse +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 + """ + float_format = re.compile("^[\-]?[1-9][0-9]*\.?[0-9]+$") + int_format = re.compile("^[\-]?[1-9][0-9]*$") + test = "" + if format == "int": + test = re.match(int_format, n) + elif format == "float": + test = re.match(float_format, n) + if test: + 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"] + for i in range(len(inputs)): + input_file = inputs[i][0] + name = inputs[i][1] + input_type = inputs[i][2] + title = c[i] + title_dict[title] = name + ids = set() + if input_type == "file": + header = inputs[i][3] + ncol = inputs[i][4] + file_content = open(input_file, "r").readlines() + + # Check if column number is in right form + if isnumber("int", ncol.replace("c", "")): + if header == "true": + file_content = [x.strip() for x in [line.split("\t")[int(ncol.replace("c", ""))-1].split(";")[0] for line in file_content[1:]]] # take only first IDs + else: + file_content = [x.strip() for x in [line.split("\t")[int(ncol.replace("c", ""))-1].split(";")[0] for line in file_content]] # take only first IDs + #print(file_content[1:13]) + else: + raise ValueError("Please fill in the right format of column number") + else: + ids = set() + file_content = inputs[i][0].split() + + ids.update(file_content) + comp_dict[title] = ids + + return comp_dict, title_dict + +def intersect(comp_dict): + """ + Calculate the intersections of input + """ + names = set(comp_dict) + for i in range(1, len(comp_dict) + 1): + for group in combinations(sorted(comp_dict), i): + others = set() + [others.add(name) for name in names if name not in group] + difference = [] + intersected = set.intersection(*(comp_dict[k] for k in group)) + n = "".join(group) + if len(others) > 0: + difference = intersected.difference(set.union(*(comp_dict[k] for k in others))) + yield group, list(intersected), list(difference) + +def diagram(comp_dict, title_dict): + """ + Create json string for jvenn diagram plot + """ + result = {} + result["name"] = {} + for k in comp_dict.keys(): + result["name"][k] = title_dict[k] + + result["data"] = {} + result["values"] = {} + for group, intersected, difference in intersect(comp_dict): + if len(group) == 1: + result["data"]["".join(group)] = 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) + elif len(group) == len(comp_dict): + result["data"]["".join(group)] = intersected + result["values"]["".join(group)] = len(intersected) + + return result + +def write_text_venn(json_result): + """ + Write intersections of input to text output file + """ + output = open("venn_diagram_text_output.txt", "w") + string = "" + lines = [] + result = dict((k, v) for k, v in json_result["data"].iteritems() if v != []) + print(result) + max_count = max(len(v) for v in result.values()) + print(max_count) + for i in range(max_count): + lines.append("") + + for i in range(max_count): + header = "" + for d in range(len(result.keys())): + data = result.keys()[d] + name = "_".join([json_result["name"][x] for x in data]) + header += name + "\t" + if len(result[data]) > i: + lines[i] += result[data][i] + "\t" + else: + lines[i] += "\t" + string += header + "\n" + string += "\n".join(lines) + print(string) + output.write(string) + output.close() + +def write_summary( summary_file, inputs): + """ + Paste json string into template file + """ + a, b = input_to_dict(inputs) + data = diagram(a, b) + write_text_venn(data) + + to_replace = { + "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" ) + 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]") + args = parser.parse_args() + + # Process + process( args )
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/venn_diagram.xml Fri Sep 15 09:32:19 2017 -0400 @@ -0,0 +1,169 @@ +<?xml version="1.0"?> +<tool id="Jvenn" name="Venn diagram plotter" version="1.0"> + <description>An integrative tool for comparing up to 6 ID lists with Venn Diagrams (based on Jvenn). + </description> + <command><![CDATA[ + python $__tool_directory__/venn_diagram.py + + #for $i, $s in enumerate($series) + --input + #if $s.se.input == "file" + "$s.se.file" "$s.se.name" "file" "$s.se.header" "$s.se.ncol" + #else + "$s.se.list" "$s.se.name" "list" + #end if + #end for + --summary "$output_summary" + ]]></command> + <inputs> + <!-- Files --> + <repeat name="series" title="Lists to compare" min="2" max="6" > + <conditional name="se" > + <param type="select" name="input" label="Please provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" > + <option value="list">Copy/paste your identifiers </option> + <option value="file">Input file containing your identifiers</option> + + </param> + <when value="file"> + <param type="data" name="file" format="txt,tabular" label="Choose a file that contains your list of IDs" /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> + <param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' /> + <param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" /> + </when> + <when value="list"> + <param type="text" name="list" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' > + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + <param type="text" name="name" value="" label="Please enter the name of this list" help="This name will be displayed on venn diagram" /> + </when> + </conditional> + </repeat> + </inputs> + <outputs> + <data format="html" name="output_summary" label="Venn diagram" from_work_dir="venn_diagram_summary.html" /> + <data format="tabular" name="output_text" label="Venn diagram text output" from_work_dir="venn_diagram_text_output.txt" /> + </outputs> + <tests> + <test> + <repeat name="series"> + <conditional name="se"> + <param name="input" value="mq_file" /> + <param name="mq_file" value="DESeq.txt" /> + <param name="header" value="false" /> + <param name="ncol" value="c1" /> + <param name="name" value="DESeq" /> + </conditional> + </repeat> + <repeat name="series"> + <conditional name="se"> + <param name="input" value="mq_file" /> + <param name="mq_file" value="FQ.txt" /> + <param name="header" value="false" /> + <param name="ncol" value="c1" /> + <param name="name" value="FQ" /> + </conditional> + </repeat> + <repeat name="series"> + <conditional name="se"> + <param name="input" value="mq_file" /> + <param name="mq_file" value="RPKM.txt" /> + <param name="header" value="false" /> + <param name="ncol" value="c1" /> + <param name="name" value="RPKM" /> + </conditional> + </repeat> + <repeat name="series"> + <conditional name="se"> + <param name="input" value="mq_file" /> + <param name="mq_file" value="TC.txt" /> + <param name="header" value="false" /> + <param name="ncol" value="c1" /> + <param name="name" value="TC" /> + </conditional> + </repeat> + <repeat name="series"> + <conditional name="se"> + <param name="input" value="mq_file" /> + <param name="mq_file" value="TMM.txt" /> + <param name="header" value="false" /> + <param name="ncol" value="c1" /> + <param name="name" value="TMM" /> + </conditional> + </repeat> + <repeat name="series"> + <conditional name="se"> + <param name="input" value="mq_file" /> + <param name="mq_file" value="UQ.txt" /> + <param name="header" value="false" /> + <param name="ncol" value="c1" /> + <param name="name" value="UQ" /> + </conditional> + </repeat> + <output name="output_summary" file="venn_diagram_summary.html" /> + <output name="output_text" file="venn_diagram_text_output.txt" /> + + </test> + </tests> + <help> + +This tool draw a venn diagram from lists/files using Jvenn plug-in (http://jvenn.toulouse.inra.fr/app/index.html). It also creates output files that contain common or specific elements between query and each compared lists/files. + +**Inputs** + +* **Query file:** A file containing different information of proteins, could be output of previous components. + +* **File of a list of IDs:** .TXT format, each line contains 1 ID + + AMY1A + + ALB + + IGKC + + CSTA + + IGHA1 + + ACTG1 + +* **List of IDs:** IDs separated by a space + AMY1A ALB IGKC CSTA IGHA1 ACTG1 + +If you choose a file, it is necessary to specify the column where you would like to perform the comparison. + +**Outputs** + +* **Summary file** (venn_diagram_summary.html): + Venn diagram: Could be downloaded as image (PNG, SVG) + +* **Venn text output file** + A text file containing common/specific elements among compared lists/files. + +----- + +.. class:: infomark + +**Authors** + +Philippe Bardou, Jérôme Mariette, Frédéric Escudié, Christophe Djemiel and Christophe Klopp. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 2014, 15:293 doi:10.1186/1471-2105-15-293 + +.. class:: infomark + +**Galaxy integration** + +T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR +Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit,Migale Bioinformatics platform + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + + </help> + <citations> + </citations> +</tool>