Mercurial > repos > proteore > proteore_reactome

annotate reactome_analysis.py @ 7:6c95f1b88627 draft

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planemo upload commit 89cd1b5f2ca7b135abfe2d9ed18bf2478a59e099-dirty
author proteore
date Tue, 05 Mar 2019 09:40:41 -0500
parents 9cc475dcd0f2
children a58dc5d4b8cd
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 import os
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2 import re
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3 import json
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4 import argparse
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5
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6 CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
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7
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8 def id_valid(identifiers):
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9 """
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10 Validate IDs if they contain special characters
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11 """
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12 res = []
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13 remove = []
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14 for id in identifiers:
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15 id = id.split(";")[0]
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16 if re.match("^[A-Za-z0-9_-]*$", id):
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17 res.append(id)
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18 else:
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19 remove.append(id)
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20 return res, remove
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21
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22 def isnumber(format, n):
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23 """
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24 Check if an variable is numeric
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25 """
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26 float_format = re.compile(r"^[-]?[1-9][0-9]*.?[0-9]+$")
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27 int_format = re.compile(r"^[-]?[1-9][0-9]*$")
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28 test = ""
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29 if format == "int":
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30 test = re.match(int_format, n)
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31 elif format == "float":
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32 test = re.match(float_format, n)
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33 if test:
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34 return True
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35 else:
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36 return False
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37
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38 def data_json(identifiers):
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39 """
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40 Submit IDs list to Reactome and return results in json format
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41 Return error in HTML format if web service is not available
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42 """
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43 trash = []
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44 if identifiers[1] == "list":
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45 ids = "\n".join(id_valid(identifiers[0].split())[0])
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46 json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1" % ids).read()
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47 if len(id_valid(identifiers[0].split())[1]) > 0:
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48 trash = id_valid(identifiers[0].split())[1]
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49 elif identifiers[1] == "file":
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50 header = identifiers[2]
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51 mq = open(identifiers[0]).readlines()
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52 if isnumber("int", identifiers[3].replace("c", "")):
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53 if header == "true":
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54 idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq[1:]]
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55 else:
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56 idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq]
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57 ids = "\n".join(id_valid(idens)[0])
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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()
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59 if len(id_valid(idens)[1]) > 0:
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60 trash = id_valid(idens)[1]
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61 #print(json_string)
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62 j = json.loads(json_string)
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63 print ("Identifiers not found: " + str(j["identifiersNotFound"]))
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64 print ("Pathways found: " + str(j["pathwaysFound"]))
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65 return json_string, trash
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66
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67 def write_output(filename, json_string, species, trash_file, trash):
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68 """
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69 Replace json result in template and print to output
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70 """
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71 template = open(os.path.join(CURRENT_DIR, "template.html"))
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72 output = open(filename, "w")
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73 try:
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74 for line in template:
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75 if "{token}" in line:
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76 line = line.replace("{species}", species)
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77 line = line.replace("{token}", json.loads(json_string)["summary"]["token"])
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78 output.write(line)
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79 except ValueError:
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80 output.write("An error occurred due to unavailability of Reactome web service. Please return later.")
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81 template.close()
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82 output.close()
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83
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84 if trash:
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85 #print(trash)
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86 trash_out = open(trash_file, "w")
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87 trash_out.write("\n".join(trash))
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88 trash_out.close()
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89
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90 def options():
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91 parser = argparse.ArgumentParser()
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92 argument = parser.add_argument("--json", nargs="+", required=True)
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93 argument = parser.add_argument("--output", default="output.html")
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94 argument = parser.add_argument("--trash", default="trash.txt")
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95 argument = parser.add_argument("--species", default="48887")
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96 args = parser.parse_args()
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97 filename = args.output
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98 json_string, trash = data_json(args.json)
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99 write_output(filename, json_string, args.species, args.trash, trash)
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100
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101 if __name__ == "__main__":
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102 options()