diff fathmm/fathmm.py @ 0:fd66648ce5f9 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fathmm/fathmm.py	Tue Oct 07 19:25:07 2014 -0400
@@ -0,0 +1,60 @@
+import requests
+import argparse
+import os
+import sys
+
+__base_url__ = "http://supfam3.cs.bris.ac.uk/FATHMM/"
+__submit_url__ = __base_url__ + "cgi-bin/submit.cgi"
+__result_url__ = __base_url__ + "cgi-bin/"
+__download_url__ = __base_url__ + "tmp/"
+__type__="CANCER" ##Hidden field to show which type of variants we are processing
+
+
+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()
+    threshold = -0.75
+    if (args.threshold):
+        threshold = float(args.threshold)
+    data = {"weighted": __type__,
+            "batch": contents,
+            "threshold": threshold
+            }
+    response = requests.post(__submit_url__, data=data)
+    if response.status_code!=200:
+        stop_err("Error processing request, got" + response.status_code)
+    text = response.text
+    split_text = text.split("window.location = ")
+    try:
+        url = split_text[1]
+        url = url.split(";")[0]
+        url = url.split("session=")[1]
+        url = url.replace("'", "").replace("./","")
+        url = __download_url__ + url + ".tab"
+    except IndexError:
+        stop_err("Unable to parse result id")
+    response = requests.get(url)
+    with open(args.output, 'wb') as fp:
+        fp.write(response.text)
+
+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 location')
+    parser.add_argument('--threshold',
+                         type=float,
+                         required=False,
+                         help='Predictions with score less than threshold are possibly cancer causing')
+    args = parser.parse_args()
+    main_web(args)