# HG changeset patch
# User proteore
# Date 1511741380 18000
# Node ID 9d4f20618ab4fe07385f2b3b7901c2e6f3f8e1fd
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
diff -r 000000000000 -r 9d4f20618ab4 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Sun Nov 26 19:09:40 2017 -0500
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+Wrapper for Jvenn plug-in
+=========================
+
+**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
+
+**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.
+
+=========================
+
+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.
diff -r 000000000000 -r 9d4f20618ab4 jvenn_template.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/jvenn_template.html Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,228 @@
+
+
+
+
+ Jvenn+
+
+ javascript is needed to display data.
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 9d4f20618ab4 test-data/DESeq.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/DESeq.txt Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,1249 @@
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diff -r 000000000000 -r 9d4f20618ab4 test-data/FQ.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/FQ.txt Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,1092 @@
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diff -r 000000000000 -r 9d4f20618ab4 test-data/RPKM.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RPKM.txt Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,417 @@
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diff -r 000000000000 -r 9d4f20618ab4 test-data/TC.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TC.txt Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,548 @@
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diff -r 000000000000 -r 9d4f20618ab4 test-data/TMM.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TMM.txt Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,1190 @@
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diff -r 000000000000 -r 9d4f20618ab4 test-data/UQ.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/UQ.txt Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,1213 @@
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diff -r 000000000000 -r 9d4f20618ab4 test-data/venn_diagram_summary.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 9d4f20618ab4 test-data/venn_diagram_text_output.txt
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+ G002469 G002001
+ G002749 G001951
+ G001929 G001819
+ G005220 G002797
+ G004088 G001771
+ G001022 G001772
+ G001604 G001554
+ G001355 G000705
+ G001606 G000704
+ G001353 G000701
+ G001210 G000951
+ G004302 G001650
+ G000637 G001651
+ G000635 G002077
+ G000631 G003075
+ G000737 G001006
+ G000827 G000259
+ G000730 G004187
+ G002120 G004565
+ G003025 G004131
+ G003342 G004136
+ G002687 G003208
+ G001289 G003611
+ G001324 G005119
+ G001325 G004762
+ G001281 G005269
+ G003938 G005268
+ G004022 G004768
+ G003931 G005264
+ G003163 G005263
+ G001517 G004299
+ G001457 G002097
+ G002051 G000311
+ G003233 G000316
+ G003791 G004612
+ G003238 G005212
+ G003480 G004349
+ G003337 G004618
+ G004470 G001136
+ G004610 G000101
+ G000358 G001045
+ G003800 G001043
+ G004657 G000005
+ G004874 G003539
+ G003808 G003220
+ G000352 G002755
+ G004625 G002453
+ G002228 G005105
+ G001711 G000030
+ G004784 G002282
+ 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
\ No newline at end of file
diff -r 000000000000 -r 9d4f20618ab4 venn_diagram.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/venn_diagram.py Sun Nov 26 19:09:40 2017 -0500
@@ -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 )
diff -r 000000000000 -r 9d4f20618ab4 venn_diagram.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/venn_diagram.xml Sun Nov 26 19:09:40 2017 -0500
@@ -0,0 +1,170 @@
+
+
+ compare lists plotting Venn Diagram (based on Jvenn).
+
+
+
+
+
+ Copy/paste your identifiers
+ Input file containing your identifiers
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+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.
+
+
+
+
+