Mercurial > repos > proteore > proteore_reactome

annotate 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
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5
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1 import os, re, json, argparse, csv
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2
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3 CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
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4
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5 def id_valid(identifiers):
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6 """
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7 Validate IDs if they contain special characters
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8 """
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9 res = []
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10 remove = []
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11 for id in identifiers:
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12 id = id.split(";")[0]
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13 if re.match("^[A-Za-z0-9_-]*$", id):
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14 res.append(id)
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15 else:
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16 remove.append(id)
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17 return res, remove
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18
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19 def isnumber(format, n):
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20 """
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21 Check if an variable is numeric
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22 """
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23 float_format = re.compile(r"^[-]?[1-9][0-9]*.?[0-9]+$")
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24 int_format = re.compile(r"^[-]?[1-9][0-9]*$")
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25 test = ""
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26 if format == "int":
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27 test = re.match(int_format, n)
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28 elif format == "float":
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29 test = re.match(float_format, n)
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30 if test:
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31 return True
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32 else:
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33 return False
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34
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35 def data_json(identifiers):
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36 """
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37 Submit IDs list to Reactome and return results in json format
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38 Return error in HTML format if web service is not available
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39 """
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40 trash = []
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41 if identifiers[1] == "list":
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42 ids = identifiers[0].split()
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43 ids = [x.split(";") for x in ids]
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44 ids = [item.strip() for sublist in ids for item in sublist if item != '']
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45 json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1" % ids).read()
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46 if len(id_valid(identifiers[0].split())[1]) > 0:
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47 trash = id_valid(identifiers[0].split())[1]
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48 elif identifiers[1] == "file":
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49 header = identifiers[2]
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50 with open(identifiers[0],"r") as mq :
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51 file_content = csv.reader(mq,delimiter="\t")
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52 file_content = list(file_content) #csv object to list
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53 ncol = identifiers[3]
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54 if isnumber("int", ncol.replace("c", "")):
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55 if header == "true":
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56 idens = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]]
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57 else:
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58 idens = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]]
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59
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60 idens = [item.strip() for sublist in idens for item in sublist if item != ''] #flat list of list of lists, remove empty items
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61 ids = "\n".join(id_valid(idens)[0])
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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()
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63 if len(id_valid(idens)[1]) > 0:
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64 trash = id_valid(idens)[1]
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65 #print(json_string)
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66 j = json.loads(json_string)
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67 print ("Identifiers not found: " + str(j["identifiersNotFound"]))
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68 print ("Pathways found: " + str(j["pathwaysFound"]))
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69 return json_string, trash
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70
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71 def write_output(filename, json_string, species, trash_file, trash):
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72 """
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73 Replace json result in template and print to output
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74 """
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75 template = open(os.path.join(CURRENT_DIR, "template.html"))
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76 output = open(filename, "w")
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77 try:
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78 for line in template:
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79 if "{token}" in line:
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80 line = line.replace("{species}", species)
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81 line = line.replace("{token}", json.loads(json_string)["summary"]["token"])
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82 output.write(line)
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83 except ValueError:
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84 output.write("An error occurred due to unavailability of Reactome web service. Please return later.")
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85 template.close()
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86 output.close()
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87
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88 if trash:
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89 #print(trash)
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90 trash_out = open(trash_file, "w")
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91 trash_out.write("\n".join(trash))
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92 trash_out.close()
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93
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94 def options():
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95 parser = argparse.ArgumentParser()
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96 argument = parser.add_argument("--json", nargs="+", required=True)
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97 argument = parser.add_argument("--output", default="output.html")
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98 argument = parser.add_argument("--trash", default="trash.txt")
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99 argument = parser.add_argument("--species", default="48887")
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100 args = parser.parse_args()
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101 filename = args.output
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102 json_string, trash = data_json(args.json)
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103 write_output(filename, json_string, args.species, args.trash, trash)
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104
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105 if __name__ == "__main__":
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106 options()