--- a/cravat_submit/cravat_submit.py	Wed Jul 18 10:32:36 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,103 +0,0 @@
-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://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://cravat.us/CRAVAT/results/" + jobid + "/" + "Variant.Result.tsv", file_1)
-urllib.urlretrieve("http://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