--- /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)
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