diff mutationassesor_web/mutation_assesor.py @ 0:e51722489ddb draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mutationassesor_web/mutation_assesor.py	Tue Oct 07 19:40:29 2014 -0400
@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+import sys
+import requests
+import os
+import argparse
+import re
+import csv
+import StringIO
+__url__ = 'http://mutationassessor.org/'
+
+
+def stop_err(msg, err=1):
+    sys.stderr.write('%s\n' % msg)
+    sys.exit(err)
+
+
+def main_web(args):
+    assert os.path.exists(args.input)
+    with open(args.input) as f:
+        contents = f.read().strip()
+    if args.hg19 is True and args.protein is True:
+        stop_err('--hg19 option conflicts with --protein')
+    if args.protein is False:
+        ## Replace tabs/space with commas
+        re.sub('[\t\s]+', ',', contents)
+    if args.hg19:
+        ## Append hg19 to each line
+        lines = contents.split('\n')
+        contents = ('\n').join(
+            map((lambda x: 'hg19,' + x),
+                lines))
+
+    payload = {'vars': contents, 'tableQ': 1}
+    request = requests.post(__url__, data=payload)
+    response = request.text
+    if request.status_code != requests.codes.ok:
+        stop_err("""Error retrieving response from server.
+                 Server returned %s .
+                 Output: %s
+                 """ % (request.status_code, response))
+    r = StringIO.StringIO(response)
+    reader = csv.reader(r, delimiter=",")
+    csv.writer(open(args.output, "wb"), delimiter='\t').writerows(reader)
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description="Process input output paths")
+    parser.add_argument('--input',
+                        type=str,
+                        required=True,
+                        help='Input file location')
+    parser.add_argument('--output',
+                        type=str,
+                        required=True,
+                        help='Output file locatio')
+    parser.add_argument('--log',
+                        type=str,
+                        required=False)
+    parser.add_argument('--hg19',
+                        action='store_true',
+                        help="""Use hg19 build.
+                        Appends 'hg19' to each input line""")
+    parser.add_argument('--protein',
+                        action='store_true',
+                        help='Inputs are in protein space')
+    args = parser.parse_args()
+    main_web(args)