# HG changeset patch
# User proteore
# Date 1511742557 18000
# Node ID 216bd2a75b1dfc8a4c4f7a8a762b132ab9418320
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
diff -r 000000000000 -r 216bd2a75b1d README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Sun Nov 26 19:29:17 2017 -0500
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+Wrapper for Reactome web service
+================================
+
+Reactome web service (https://reactome.org)
+
+**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.
+
+================================
+
+Reactome software provides service of creating diagram representing the relations between the biological processes. This tool allows linking to Reactome web service with pre-loaded data from a list of IDs, a file containing IDs or from a column of a complexed file.
+
+**For the rows that have more than 1 ID, only the first one is taken into account**
+
+**This tool only accepts letters (a-z or A-Z), numbers (0-9) and 3 characters "." "-" "_" for IDs. If there is ID containing other than these characters, it will be removed from the queue and placed in "Invalid identifiers" file**
diff -r 000000000000 -r 216bd2a75b1d reactome_analysis.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/reactome_analysis.py Sun Nov 26 19:29:17 2017 -0500
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+import os
+import re
+import json
+import argparse
+
+CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
+
+def id_valid(identifiers):
+ """
+ Validate IDs if they contain special characters
+ """
+ res = []
+ remove = []
+ for id in identifiers:
+ id = id.split(";")[0]
+ if re.match("^[A-Za-z0-9_-]*$", id):
+ res.append(id)
+ else:
+ remove.append(id)
+ return res, remove
+
+def isnumber(format, n):
+ """
+ Check if an variable is numeric
+ """
+ float_format = re.compile("^[\-]?[1-9][0-9]*\.?[0-9]+$")
+ int_format = re.compile("^[\-]?[1-9][0-9]*$")
+ test = ""
+ if format == "int":
+ test = re.match(int_format, n)
+ elif format == "float":
+ test = re.match(float_format, n)
+ if test:
+ return True
+ else:
+ return False
+
+def data_json(identifiers):
+ """
+ Submit IDs list to Reactome and return results in json format
+ Return error in HTML format if web service is not available
+ """
+ trash = []
+ if identifiers[1] == "list":
+ ids = "\n".join(id_valid(identifiers[0].split())[0])
+ #print(ids)
+ #print("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids)
+ json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids).read()
+ if len(id_valid(identifiers[0].split())[1]) > 0:
+ trash = id_valid(identifiers[0].split())[1]
+ elif identifiers[1] == "file":
+ header = identifiers[2]
+ mq = open(identifiers[0]).readlines()
+ if isnumber("int", identifiers[3].replace("c", "")):
+ if header == "true":
+ idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq[1:]]
+ else:
+ idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq]
+ ids = "\n".join(id_valid(idens)[0])
+ #print(ids)
+ #print("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids)
+ json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids).read()
+ if len(id_valid(idens)[1]) > 0:
+ trash = id_valid(idens)[1]
+ print(json_string)
+ return json_string, trash
+
+def write_output(filename, json_string, trash_file, trash):
+ """
+ Replace json result in template and print to output
+ """
+ template = open(os.path.join(CURRENT_DIR, "template.html"))
+ output = open(filename, "w")
+ try:
+ for line in template:
+ if "{token}" in line:
+ line = line.replace("{token}", json.loads(json_string)["summary"]["token"])
+ output.write(line)
+ except ValueError:
+ output.write("An error occurred due to unavailability of Reactome web service. Please return later.")
+ template.close()
+ output.close()
+
+ trash_out = open(trash_file, "w")
+ trash_out.write("\n".join(trash))
+ trash_out.close()
+
+def options():
+ parser = argparse.ArgumentParser()
+ argument = parser.add_argument("--json", nargs="+", required=True)
+ argument = parser.add_argument("--output", default="output.html")
+ argument = parser.add_argument("--trash", default="trash.txt")
+ args = parser.parse_args()
+ filename = args.output
+ json_string, trash = data_json(args.json)
+ write_output(filename, json_string, args.trash, trash)
+
+if __name__ == "__main__":
+ options()
diff -r 000000000000 -r 216bd2a75b1d reactome_analysis.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/reactome_analysis.xml Sun Nov 26 19:29:17 2017 -0500
@@ -0,0 +1,63 @@
+
+ query Reactome with your IDs list
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diff -r 000000000000 -r 216bd2a75b1d template.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/template.html Sun Nov 26 19:29:17 2017 -0500
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+ Connection to the Reactome Analysis Service
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+ Connection to the Reactome Analysis Service
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+ Please click the button to execute the analysis:
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diff -r 000000000000 -r 216bd2a75b1d test-data/UnipIDs.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/UnipIDs.txt Sun Nov 26 19:29:17 2017 -0500
@@ -0,0 +1,25 @@
+P04637
+P08246
+P63244
+P10275
+P00533
+Q14524
+P05067
+P35555
+P35222
+O95273
+P00451
+P38398
+Q05086
+Q12802
+P68871
+P04585
+Q96EB6
+Q9NYL2
+P31749
+P01137
+Q5S007
+Q08379
+P02649
+P35498
+P12931
diff -r 000000000000 -r 216bd2a75b1d test-data/reactome_invalide_ids.txt
diff -r 000000000000 -r 216bd2a75b1d test-data/reactome_output.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reactome_output.html Sun Nov 26 19:29:17 2017 -0500
@@ -0,0 +1,48 @@
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+ Connection to the Reactome Analysis Service
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+ Connection to the Reactome Analysis Service
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+ Please click the button to execute the analysis:
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