# HG changeset patch # User in_silico # Date 1528819614 14400 # Node ID 338d106513fd712db4f6edeb0a0d22a098f21d1b # Parent e6c1dc59a01f1daff575934b0fe87522553d700c Uploaded diff -r e6c1dc59a01f -r 338d106513fd cravat_convert/cravat_convert.xml --- a/cravat_convert/cravat_convert.xml Tue Jun 12 12:03:50 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ - - Converts a VCF format file to a Cravat format file - cravat_convert.py -i $input -o $output - - - - - - - - - - - - - Converts a VCF format file to a Cravat format file - - - - diff -r e6c1dc59a01f -r 338d106513fd cravat_submit/cravat_submit.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_submit/cravat_submit.py Tue Jun 12 12:06:54 2018 -0400 @@ -0,0 +1,103 @@ +import requests +import json +import time +import urllib +import sys +import csv + +input_filename = sys.argv[1] +input_select_bar = sys.argv[2] +output_filename = sys.argv[3] + +# HACK: Input args corrections. +if input_select_bar == "None": + # The server represents an analyses of None as ""; however, submitting a blank string on command line throws off arg position + input_select_bar = "" + # The server represents the "Vest and Chasm" analyses as "VEST;CHASM; however, galaxy converts the semi-colon to an 'X'. Switch it back. +elif input_select_bar == "VESTXCHASM": + input_select_bar = "VEST;CHASM" + +write_header = True + +#plugs in params to given URL +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}) +#,'analysis':input_select_bar,'functionalannotation': "on"}) +#Makes the data a json dictionary, takes out only the job ID +jobid = json.loads(submit.text)['jobid'] +#out_file.write(jobid) +submitted = json.loads(submit.text)['status'] +#out_file.write('\t' + submitted) + +#loops until we find a status equal to Success, then breaks +while True: + check = requests.get('http://staging.cravat.us/CRAVAT/rest/service/status', params={'jobid': jobid}) + status = json.loads(check.text)['status'] + resultfileurl = json.loads(check.text)['resultfileurl'] + #out_file.write(str(status) + ', ') + if status == 'Success': + #out_file.write('\t' + resultfileurl) + break + else: + time.sleep(2) + +#out_file.write('\n') + +#creates three files +file_1 = time.strftime("%H:%M") + '_Z_Variant_Result.tsv' +file_2 = time.strftime("%H:%M") + '_Z_Additional_Details.tsv' +file_3 = time.strftime("%H:%M") + 'Combined_Variant_Results.tsv' + + +#Download the two results +urllib.urlretrieve("http://staging.cravat.us/CRAVAT/results/" + jobid + "/" + "Variant.Result.tsv", file_1) +urllib.urlretrieve("http://staging.cravat.us/CRAVAT/results/" + jobid + "/" + "Variant_Additional_Details.Result.tsv", file_2) + +headers = [] +duplicates = [] + +#opens the Variant Result file and the Variant Additional Details file as csv readers, then opens the output file (galaxy) as a writer +with open(file_1) as tsvin_1, open(file_2) as tsvin_2, open(output_filename, 'wb') as tsvout: + tsvreader_1 = csv.reader(tsvin_1, delimiter='\t') + tsvreader_2 = csv.reader(tsvin_2, delimiter='\t') + tsvout = csv.writer(tsvout, delimiter='\t') + +#loops through each row in the Variant Additional Details file + for row in tsvreader_2: + #sets row_2 equal to the same row in Variant Result file + row_2 = tsvreader_1.next() + #checks if row is empty or if the first term contains '#' + if row == [] or row[0][0] == '#': + continue + #checks if the row begins with input line + if row[0] == 'Input line': + #Goes through each value in the headers list in VAD + for value in row: + #Adds each value into headers + headers.append(value) + #Loops through the Keys in VR + for value in row_2: + #Checks if the value is already in headers + if value in headers: + continue + #else adds the header to headers + else: + headers.append(value) + + print headers + tsvout.writerow(headers) + + + else: + + cells = [] + #Goes through each value in the next list + for value in row: + #adds it to cells + cells.append(value) + #Goes through each value from the VR file after position 11 (After it is done repeating from VAD file) + for value in row_2[11:]: + #adds in the rest of the values to cells + cells.append(value) + + print cells + tsvout.writerow(cells) \ No newline at end of file diff -r e6c1dc59a01f -r 338d106513fd cravat_submit/cravat_submit.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_submit/cravat_submit.xml Tue Jun 12 12:06:54 2018 -0400 @@ -0,0 +1,34 @@ + + Submits, checks for, and retrieves data for cancer annotation + cravat_submit.py $input $dropdown $output + + + + + + + + + + + + + + + + + + + + + + + + + + + + This tool submits, checks for, and retrieves data for cancer annotation. + + +