Merge pull request #10 from NCIP/devel

COSMIC pulling CANCER snps in cancer.vcf

src/annotate_with_cravat.py

@@ -13,7 +13,7 @@
 import os
 import requests
 import time
-import urllib
+import urllib.request
 
 # Constants
 str_response_job_id = "jobid"
@@ -55,7 +55,7 @@ def func_check_job(str_json_id):
 
  # Send file over to service
  response_check_job = requests.get("http://www.cravat.us/CRAVAT/rest/service/status", params={ str_response_job_id: str_json_id })
- return response_check_job.json()
+ return(response_check_job.json())
 
 def func_download_cravat_result(str_cravat_url, str_download_location):
  """
@@ -69,11 +69,11 @@ def func_download_cravat_result(str_cravat_url, str_download_location):
 
  # Download Cravat result
  try:
- urllib.urlretrieve(str_cravat_url, str_download_location)
- return True
+ urllib.request.urlretrieve(str_cravat_url, str_download_location)
+ return(True)
  except IOError:
- print "annotate_with_cravat::Error in retrieving results. " + str(IOError)
- return False
+ print("annotate_with_cravat::Error in retrieving results. " + str(IOError))
+ return(False)
 
 def func_get_cravat_response(str_json_id, i_max_attempts, i_wait):
  """
@@ -87,26 +87,26 @@ def func_get_cravat_response(str_json_id, i_max_attempts, i_wait):
  : int
  """
 
- for x_attempt in xrange(i_max_attempts):
- print "annotate_with_cravat::Attempting to get CRAVAT response. Attempt " + str(x_attempt + 1)
+ for x_attempt in range(i_max_attempts):
+ print("annotate_with_cravat::Attempting to get CRAVAT response. Attempt " + str(x_attempt + 1))
  time.sleep(i_wait)
  response_json = func_check_job(str_json_id)
  if not response_json:
- print "annotate_with_cravat::Error did not get a response from CRAVAT"
+ print("annotate_with_cravat::Error did not get a response from CRAVAT")
  return(None)
  str_success = str(response_json.get(str_response_status, None))
  if (not str_success) or (str_success in lstr_response_fail):
- print " ".join(["annotate_with_cravat::Error was not successful in getting info from CRAVAT.",
+ print (" ".join(["annotate_with_cravat::Error was not successful in getting info from CRAVAT.",
  "Job id =" + str(str_json_id) + ".",
  "Success =" + str(str_success) + ".",
- response_json.get(str_response_log, "")])
+ response_json.get(str_response_log, "")]))
  return(None)
  if str_success == str_response_pass:
- print "annotate_with_cravat:: Reponse URL on success: " + str(response_json)
+ print("annotate_with_cravat:: Reponse URL on success: " + str(response_json))
  return response_json.get(str_response_url, None)
- print " ".join(["annotate_with_cravat::Error gave up on CRAVAT after " + str(i_max_attempts * i_wait) + " seconds.",
+ print(" ".join(["annotate_with_cravat::Error gave up on CRAVAT after " + str(i_max_attempts * i_wait) + " seconds.",
  "Job id =" + str(str_json_id) + ".",
- "Success =" + str(str_success) + "."])
+ "Success =" + str(str_success) + "."]))
  return(None)
 
 
@@ -140,10 +140,10 @@ def func_request_cravat_service(str_vcf_path, str_analysis,
  response_cravat = requests.post("http://cravat.us/CRAVAT/rest/service/submit",
  files={"inputfile": open(str_vcf_path)},
  data=pyld_request)
- print response_cravat
+ print(response_cravat)
  json_response = response_cravat.json()
  # Get return (job id)
- return json_response.get(str_response_job_id, None)
+ return(json_response.get(str_response_job_id, None))
 
 # Ensure the extention to the output directory is zip
 if not os.path.splitext(args_call.str_output_dir)[1] == ".zip":
@@ -156,29 +156,29 @@ def func_request_cravat_service(str_vcf_path, str_analysis,
  args_call.f_hg_19,
  args_call.str_email)
 if not str_job_id:
- print " ".join(["annotate_with_cravat::Error Job id not found.",
- "Job id =" + str(str_job_id)])
+ print(" ".join(["annotate_with_cravat::Error Job id not found.",
+ "Job id =" + str(str_job_id)]))
  exit(100)
 
 # Wait for result
 str_download_url = func_get_cravat_response(str_job_id,
  args_call.i_max_attempts,
  args_call.i_wait)
 if not str_download_url:
- print " ".join(["annotate_with_cravat::Error did no",
+ print(" ".join(["annotate_with_cravat::Error did no",
  "recieve valid URL download.",
  "Job id =" + str(str_job_id) + ".",
- "URL =" + str(str_download_url) + "."])
+ "URL =" + str(str_download_url) + "."]))
  exit(101)
 
 # Get zip file
 f_success = func_download_cravat_result(str_download_url,
  args_call.str_output_dir)
-print "annotate_with_cravat:: Success = " + str(f_success)
+print("annotate_with_cravat:: Success = " + str(f_success))
 if not f_success:
- print " ".join(["annotate_with_cravat::Error,",
+ print(" ".join(["annotate_with_cravat::Error,",
  "could not download data in URL.",
  "Job id =" + str(str_job_id) + ".",
  "URL =" + str(str_download_url) + ".",
- "Download =" + str(args_call.str_output_dir) + "."])
+ "Download =" + str(args_call.str_output_dir) + "."]))
  exit(102)

src/filter_vcf_for_cancer.py

@@ -60,7 +60,7 @@ def func_split_token(str_token):
 
 # Get handle
 str_input_ext = os.path.splitext(args.str_input_file)[1]
-hndl_vcf = gzip.open(args.str_input_file, "rb") if str_input_ext == ".gz" else open(args.str_input_file, "rb")
+hndl_vcf = gzip.open(args.str_input_file, "rt") if str_input_ext == ".gz" else open(args.str_input_file, "r")
 
 # Read in vcf file
 if args.str_input_file:

src/filter_vcf_for_predictions.py

@@ -56,7 +56,7 @@ def func_split_token(str_token):
 
 # Get handle
 str_input_ext = os.path.splitext(args.str_input_file)[1]
-hndl_vcf = gzip.open(args.str_input_file, "rb") if str_input_ext == ".gz" else open(args.str_input_file, "rb")
+hndl_vcf = gzip.open(args.str_input_file, "rt") if str_input_ext == ".gz" else open(args.str_input_file, "rb")
 
 # Read in vcf file
 if args.str_input_file:
@@ -74,7 +74,7 @@ def func_split_token(str_token):
  # Parse INFO tokens
  dict_info_tokens = dict([func_split_token(str_token) for str_token
  in lstr_line[I_INFO_INDEX].split(CHR_INFO_DELIMITER)])
- print dict_info_tokens
+ print(dict_info_tokens)
  # Keep everything that is a COSMIC ID at this point.
  # Otherwise require CRAVAT or VEST to have an annotation.
  if STR_CHASM_FDR in dict_info_tokens: