Mercurial > repos > in_silico > cravat_score_and_annotate
diff cravat_submit/cravat_submit.py @ 13:2c9208fe16a0 draft
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author | in_silico |
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date | Mon, 30 Jul 2018 13:22:46 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_submit/cravat_submit.py Mon Jul 30 13:22:46 2018 -0400 @@ -0,0 +1,170 @@ +from __future__ import print_function +import requests +import json +import time +from urllib.request import urlretrieve +import sys +import csv +import argparse + +""" +Tool's email: +usernmae: cravatgalaxy@gmail.com +password: chicken_quesadilla +""" + +email = 'cravatgalaxy@gmail.com' + +class CravatSubmissionException(Exception): + def __init__(self, message): + super(CravatSubmissionException, self).__init__(message) + +class CravatSubmission(object): + + def get_cmd_args(self, argv): + parser = argparse.ArgumentParser() + parser.add_argument('path', + help="Path to python module") + parser.add_argument('--input', + '-i', + required = True, + help='Input path to a cravat file for querying',) + parser.add_argument('--output', + '-o', + default = None, + help = 'Output path to write results from query') + parser.add_argument('--analysis', + '-a', + required=True, + help = "Cravat analysis. Should be 'VEST', 'CHASM', 'NONE', or 'VEST;CHASM'") + return parser.parse_args(argv) + + def is_valid_analysis(self, analysis): + """: Test if analysis is a recognized value""" + analyses = ["VEST", "CHASM", "VEST;CHASM", ""] + return analysis in analyses + + def is_skippable(self, s): + """: Test if a line (str or list/tuple) is skippable, a.k.a. a header or blank line""" + if not isinstance(s, str): + raise CravatSubmissionException("is_skippable accepts a string") + skippable = s == "" \ + or s[0] == "#" \ + or s.startswith('"#For more information on CRAVAT') \ + or s.isspace() + return skippable + + def parse(self, s, sep='\t'): + """: Convert string line to an array of values""" + return s.strip().split(sep) + + def unparse(self, array, sep='\t', newline='\n'): + """: Convert an array of values to a writable string line""" + return sep.join([str(i) for i in array]) + newline + + def get_headers(self, path, pattern='Input line', sep='\t'): + """: Get the headers from a Results/Details file obtained from by a finished Cravat submission""" + with open(path, 'r') as f: + for line in f: + if line.startswith(pattern): + return self.parse(line) + return None + + def create_index(self, path, prop='Input line'): + """ + : Create an index of seek/tell positions in file associated to a line value. Used to record + : the location of lines betwen two files that are associated with each other without reading entire + : files into memory. + """ + headers = self.get_headers(path) + if prop not in headers: + raise CravatSubmissionException("Index retrievel property not found in headers") + prop_loc = headers.index(prop) + index = {} + with open(path, 'r') as f: + pos = 0 + line = f.readline() + while line != "": + if not self.is_skippable(line): + parsed = self.parse(line) + if not parsed == headers: + index[parsed[prop_loc]] = pos + pos = f.tell() + line = f.readline() + return index + + def get_header_val_dict(self, headers, vals): + """: Associate an array of header keys to an array of values.""" + return { header:val for (header, val) in zip(headers, vals) } + + def write_results(self, results_path, details_path, out_path, write_headers=True): + """ + : Using the paths to the Results and Details file from a Cravat Sumbission, + : write the output file. + """ + results_headers = self.get_headers(results_path) + details_headers = self.get_headers(details_path) + if results_headers == None \ + or details_headers == None: + raise CravatSubmissionException("Unable to intepret headers in Results or Details submission files") + headers = results_headers + headers.extend(filter(lambda x: x not in headers, details_headers)) + results_index = self.create_index(results_path) + details_index = self.create_index(details_path) + with open(results_path, 'r') as results_file, \ + open(details_path, 'r') as details_file, \ + open(out_path, 'w') as out_file: + if write_headers: + out_file.write(self.unparse(headers)) + for line_id, file_pos in results_index.items(): + results_file.seek(file_pos) + results_vals = self.parse(results_file.readline()) + results_dict = self.get_header_val_dict(results_headers, results_vals) + if line_id in details_index: + details_file.seek(details_index[line_id]) + details_vals = self.parse(details_file.readline()) + details_dict = self.get_header_val_dict(details_headers, details_vals) + # On a repeated entry, the Details value will overwrite Results value + results_dict.update(details_dict) + line = [ results_dict.get(header, 'None') for header in headers ] + out_file.write(self.unparse(line)) + + def submit(self, in_path, analysis): + """: Make a POST request to submit a job to production CRAVAT server.""" + if not self.is_valid_analysis(analysis): + raise ValueError("Did not get valid analyses.") + # Create post request to submit job to CRAVAT production server + submit = requests.post('http://cravat.us/CRAVAT/rest/service/submit', + files={'inputfile' : open(in_path)}, + data={'email' : email, + 'analyses' : analysis}) + # Check job run status in loop until status is 'Success' + jobid = json.loads(submit.text)['jobid'] + while True: + check = requests.get('http://cravat.us/CRAVAT/rest/service/status', params={'jobid': jobid}) + status = json.loads(check.text)['status'] + print(status) + if status == 'Success': + break + else: + time.sleep(2) + # Download completed job results to local files + timestamp = time.strftime("%Y-%m-%d_%H-%M-%S_") + results_path = 'Z_Variant_Result' + timestamp + '.tsv' + details_path = 'Z_Additional_Details' + timestamp + '.tsv' + urlretrieve("http://cravat.us/CRAVAT/results/" + jobid + "/" + "Variant.Result.tsv", + filename=results_path) + urlretrieve("http://cravat.us/CRAVAT/results/" + jobid + "/" + "Variant_Additional_Details.Result.tsv", + filename=details_path) + return results_path, details_path + +if __name__ == "__main__": + submission = CravatSubmission() + cmd_args = submission.get_cmd_args(sys.argv) + # Galaxy converts semi-colons to X's. Switch it back + analysis = cmd_args.analysis + if analysis == "VESTXCHASM": + analysis = "VEST;CHASM" + results_path, details_path = submission.submit(cmd_args.input, analysis) + #submission.write_results('Results_test.tsv', 'Details_test.tsv', 'Out_test.tsv') + submission.write_results(results_path, details_path, cmd_args.output) \ No newline at end of file