Mercurial > repos > proteore > proteore_reactome

comparison reactome_analysis.py @ 5:34097acf457c draft

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planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
author proteore
date Thu, 27 Jun 2019 04:21:19 -0400
parents 988a6f43acdb
children eb051cba2bda
comparison
equal deleted inserted replaced
4:113cce3fc379 5:34097acf457c
1 import os 1 import os, re, json, argparse, csv
2 import re
3 import json
4 import argparse
5 2
6 CURRENT_DIR = os.path.dirname(os.path.abspath(__file__)) 3 CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
7 4
8 def id_valid(identifiers): 5 def id_valid(identifiers):
9 """ 6 """
40 Submit IDs list to Reactome and return results in json format 37 Submit IDs list to Reactome and return results in json format
41 Return error in HTML format if web service is not available 38 Return error in HTML format if web service is not available
42 """ 39 """
43 trash = [] 40 trash = []
44 if identifiers[1] == "list": 41 if identifiers[1] == "list":
45 ids = "\n".join(id_valid(identifiers[0].split())[0]) 42 ids = identifiers[0].split()
43 ids = [x.split(";") for x in ids]
44 ids = [item.strip() for sublist in ids for item in sublist if item != '']
46 json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1" % ids).read() 45 json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1" % ids).read()
47 if len(id_valid(identifiers[0].split())[1]) > 0: 46 if len(id_valid(identifiers[0].split())[1]) > 0:
48 trash = id_valid(identifiers[0].split())[1] 47 trash = id_valid(identifiers[0].split())[1]
49 elif identifiers[1] == "file": 48 elif identifiers[1] == "file":
50 header = identifiers[2] 49 header = identifiers[2]
51 mq = open(identifiers[0]).readlines() 50 with open(identifiers[0],"r") as mq :
52 if isnumber("int", identifiers[3].replace("c", "")): 51 file_content = csv.reader(mq,delimiter="\t")
53 if header == "true": 52 file_content = list(file_content) #csv object to list
54 idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq[1:]] 53 ncol = identifiers[3]
55 else: 54 if isnumber("int", ncol.replace("c", "")):
56 idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq] 55 if header == "true":
57 ids = "\n".join(id_valid(idens)[0]) 56 idens = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]]
58 json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1 2> stderr" % ids).read() 57 else:
59 if len(id_valid(idens)[1]) > 0: 58 idens = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]]
60 trash = id_valid(idens)[1] 59
60 idens = [item.strip() for sublist in idens for item in sublist if item != ''] #flat list of list of lists, remove empty items
61 ids = "\n".join(id_valid(idens)[0])
62 json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1 2> stderr" % ids).read()
63 if len(id_valid(idens)[1]) > 0:
64 trash = id_valid(idens)[1]
61 #print(json_string) 65 #print(json_string)
62 j = json.loads(json_string) 66 j = json.loads(json_string)
63 print ("Identifiers not found: " + str(j["identifiersNotFound"])) 67 print ("Identifiers not found: " + str(j["identifiersNotFound"]))
64 print ("Pathways found: " + str(j["pathwaysFound"])) 68 print ("Pathways found: " + str(j["pathwaysFound"]))
65 return json_string, trash 69 return json_string, trash