Mercurial > repos > in_silico > cravat_score_and_annotate

changeset 2:cdd97b06c802 draft

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Uploaded
author in_silico
date Wed, 19 Jul 2017 14:58:50 -0400
parents 9c6b7291c4e6
children 0ff2d655068c
files cravat_score_and_annotate-9c6b7291c4e6/cravat_submit.py cravat_score_and_annotate-9c6b7291c4e6/cravat_submit.xml cravat_submit.py cravat_submit.xml
diffstat 4 files changed, 168 insertions(+), 168 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_score_and_annotate-9c6b7291c4e6/cravat_submit.py	Wed Jul 19 14:58:50 2017 -0400
@@ -0,0 +1,134 @@
+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]
+
+#in_file = open('input_call.txt', "r")    
+#out_file = open('output_call.txt', "w")
+
+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)
+            
+            
+            
+            
+
+            
+            
+            
+            
+  
+    
+            
+        
+         
+        
+        
+            
+            
+            
+       
+            
+    
+
+#a = 'col1\tcol2\tcol3'
+#header_list = a.split('\t')
+
+#loop through the two results, when you first hit header you print out the headers in tabular form
+#Print out each header only once
+#Combine both headers into one output file
+#loop through the rest of the data and assign each value to its assigned header
+#combine this all into one output file
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cravat_score_and_annotate-9c6b7291c4e6/cravat_submit.xml	Wed Jul 19 14:58:50 2017 -0400
@@ -0,0 +1,34 @@
+<tool id="cravat_submit" name="CRAVAT Submit, Check, and Retrieve" version="0.1.0">
+    <description>Submits, checks for, and retrieves data for cancer annotation</description>
+  <command interpreter="python">cravat_submit.py $input $dropdown $output</command>
+  
+  
+  <inputs>
+  
+    <param format="tabular" name="input" type="data" label="Source file"> </param>
+    <param format="tabular" name="dropdown" type="select" label="Analysis Program">
+      <option value="">None</option>
+      <option value="VEST">VEST</option>
+      <option value="CHASM">CHASM</option>
+      <option value="VEST;CHASM">VEST and CHASM</option>
+    </param>
+    
+    
+  </inputs>
+  
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="fa_gc_content_input.fa"/>
+      <output name="out_file1" file="fa_gc_content_output.txt"/>
+    </test>
+  </tests>
+
+  <help>
+ This tool submits, checks for, and retrieves data for cancer annotation.
+  </help>
+
+</tool>
--- a/cravat_submit.py	Wed Jul 19 14:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,134 +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]
-
-#in_file = open('input_call.txt', "r")    
-#out_file = open('output_call.txt', "w")
-
-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)
-            
-            
-            
-            
-
-            
-            
-            
-            
-  
-    
-            
-        
-         
-        
-        
-            
-            
-            
-       
-            
-    
-
-#a = 'col1\tcol2\tcol3'
-#header_list = a.split('\t')
-
-#loop through the two results, when you first hit header you print out the headers in tabular form
-#Print out each header only once
-#Combine both headers into one output file
-#loop through the rest of the data and assign each value to its assigned header
-#combine this all into one output file
-
-
-
-
-
--- a/cravat_submit.xml	Wed Jul 19 14:57:54 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-<tool id="cravat_submit" name="CRAVAT Submit, Check, and Retrieve" version="0.1.0">
-    <description>Submits, checks for, and retrieves data for cancer annotation</description>
-  <command interpreter="python">cravat_submit.py $input $dropdown $output</command>
-  
-  
-  <inputs>
-  
-    <param format="tabular" name="input" type="data" label="Source file"> </param>
-    <param format="tabular" name="dropdown" type="select" label="Analysis Program">
-      <option value="">None</option>
-      <option value="VEST">VEST</option>
-      <option value="CHASM">CHASM</option>
-      <option value="VEST;CHASM">VEST and CHASM</option>
-    </param>
-    
-    
-  </inputs>
-  
-  <outputs>
-    <data format="tabular" name="output" />
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="input" value="fa_gc_content_input.fa"/>
-      <output name="out_file1" file="fa_gc_content_output.txt"/>
-    </test>
-  </tests>
-
-  <help>
- This tool submits, checks for, and retrieves data for cancer annotation.
-  </help>
-
-</tool>