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1 import requests
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2 import json
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3 import time
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4 import urllib
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5 import sys
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6 import csv
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7
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8 input_filename = sys.argv[1]
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9 input_select_bar = sys.argv[2]
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10 output_filename = sys.argv[3]
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11
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12 # HACK: Input args corrections.
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13 if input_select_bar == "None":
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14 # The server represents an analyses of None as ""; however, submitting a blank string on command line throws off arg position
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15 input_select_bar = ""
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16 # The server represents the "Vest and Chasm" analyses as "VEST;CHASM; however, galaxy converts the semi-colon to an 'X'. Switch it back.
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17 elif input_select_bar == "VESTXCHASM":
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18 input_select_bar = "VEST;CHASM"
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19
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20 write_header = True
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21
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22 #plugs in params to given URL
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23 submit = requests.post('http://staging.cravat.us/CRAVAT/rest/service/submit', files={'inputfile':open(input_filename)}, data={'email':'znylund@insilico.us.com', 'analyses': input_select_bar})
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24 #,'analysis':input_select_bar,'functionalannotation': "on"})
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25 #Makes the data a json dictionary, takes out only the job ID
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26 jobid = json.loads(submit.text)['jobid']
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27 #out_file.write(jobid)
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28 submitted = json.loads(submit.text)['status']
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29 #out_file.write('\t' + submitted)
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30
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31 #loops until we find a status equal to Success, then breaks
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32 while True:
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33 check = requests.get('http://staging.cravat.us/CRAVAT/rest/service/status', params={'jobid': jobid})
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34 status = json.loads(check.text)['status']
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35 resultfileurl = json.loads(check.text)['resultfileurl']
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36 #out_file.write(str(status) + ', ')
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37 if status == 'Success':
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38 #out_file.write('\t' + resultfileurl)
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39 break
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40 else:
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41 time.sleep(2)
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42
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43 #out_file.write('\n')
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44
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45 #creates three files
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46 file_1 = time.strftime("%H:%M") + '_Z_Variant_Result.tsv'
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47 file_2 = time.strftime("%H:%M") + '_Z_Additional_Details.tsv'
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48 file_3 = time.strftime("%H:%M") + 'Combined_Variant_Results.tsv'
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49
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50
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51 #Download the two results
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52 urllib.urlretrieve("http://staging.cravat.us/CRAVAT/results/" + jobid + "/" + "Variant.Result.tsv", file_1)
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53 urllib.urlretrieve("http://staging.cravat.us/CRAVAT/results/" + jobid + "/" + "Variant_Additional_Details.Result.tsv", file_2)
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54
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55 headers = []
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56 duplicates = []
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57
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58 #opens the Variant Result file and the Variant Additional Details file as csv readers, then opens the output file (galaxy) as a writer
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59 with open(file_1) as tsvin_1, open(file_2) as tsvin_2, open(output_filename, 'wb') as tsvout:
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60 tsvreader_1 = csv.reader(tsvin_1, delimiter='\t')
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61 tsvreader_2 = csv.reader(tsvin_2, delimiter='\t')
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62 tsvout = csv.writer(tsvout, delimiter='\t')
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63
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64 #loops through each row in the Variant Additional Details file
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65 for row in tsvreader_2:
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66 #sets row_2 equal to the same row in Variant Result file
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67 row_2 = tsvreader_1.next()
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68 #checks if row is empty or if the first term contains '#'
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69 if row == [] or row[0][0] == '#':
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70 continue
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71 #checks if the row begins with input line
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72 if row[0] == 'Input line':
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73 #Goes through each value in the headers list in VAD
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74 for value in row:
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75 #Adds each value into headers
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76 headers.append(value)
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77 #Loops through the Keys in VR
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78 for value in row_2:
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79 #Checks if the value is already in headers
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80 if value in headers:
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81 continue
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82 #else adds the header to headers
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83 else:
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84 headers.append(value)
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85
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86 print headers
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87 tsvout.writerow(headers)
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88
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89
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90 else:
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91
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92 cells = []
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93 #Goes through each value in the next list
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94 for value in row:
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95 #adds it to cells
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96 cells.append(value)
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97 #Goes through each value from the VR file after position 11 (After it is done repeating from VAD file)
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98 for value in row_2[11:]:
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99 #adds in the rest of the values to cells
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100 cells.append(value)
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101
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102 print cells
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103 tsvout.writerow(cells) |
