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1 #!/usr/bin/env python
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2 """
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3 Script to interact with Ensemble Variant Effect Predictor(VEP)
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4 webservice
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5
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6
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7 The MIT License (MIT)
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8
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9 Copyright (c) 2014 Saket Choudhary<saketkc@gmail.com, skchoudh@usc.edu>
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10
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11 Permission is hereby granted, free of charge, to any person obtaining a copy
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12 of this software and associated documentation files (the "Software"), to deal
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13 in the Software without restriction, including without limitation the rights
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14 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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15 copies of the Software, and to permit persons to whom the Software is
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16 furnished to do so, subject to the following conditions:
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17
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18 The above copyright notice and this permission notice shall be included in
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19 all copies or substantial portions of the Software.
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20
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21 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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22 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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23 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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24 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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25 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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26 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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27 THE SOFTWARE.
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28
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29 """
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30 import argparse
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31 import requests
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32 import sys
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33 import time
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34 import vcf
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35
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36 URL = 'http://grch37.rest.ensembl.org/vep/human/region/{}:{}-{}/{}?content-type=application/json&protein=1'
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37
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38 class VEPRestClient:
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39
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40 def __init__(self, input_file, output_file):
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41 self.pending_urls = []
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42 vcf_reader = vcf.Reader(open(input_file, 'r'))
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43 self.output_file = output_file
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44 for record in vcf_reader:
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45 url = URL.format(record.CHROM, record.POS, record.POS, ("").join([str(x) for x in record.ALT]))
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46 key = "{}:{}-{}-{}".format(record.CHROM, record.POS, record.POS, ("").join([str(x) for x in record.ALT]))
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47 self.pending_urls.append((key, url))
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48
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49 def submit(self):
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50 protein_variants = {}
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51 for record in self.pending_urls:
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52 vcf_key = record[0]
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53 url = record[1]
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54 request = requests.get(url)
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55 time_delay = None
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56 try:
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57 retry_delay = request.headers['Retry-After']
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58 time_delay = retry_delay
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59 except KeyError:
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60 pass
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61 response = None
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62 if time_delay:
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63 time.sleep(time_delay)
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64 request = requests.get(url)
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65 try:
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66 response = request.json()[0]
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67 except Exception as e:
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68 #TODO Better error handling
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69 print e
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70 if not response:
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71 continue
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72 variants = response['transcript_consequences']
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73 consequence = ""
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74 for variant in variants:
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75 consequence = ""
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76 protein_id = None
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77 protein_start = None
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78 try:
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79 protein_id = variant['protein_id']
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80 except KeyError:
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81 pass
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82 try:
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83 protein_start = variant['protein_start']
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84 except KeyError:
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85 pass
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86 if protein_id:
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87 if protein_id.startswith('ENSP'):
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88 if variant['protein_id'] not in protein_variants.keys():
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89 protein_variants[protein_id] = []
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90 consequence += protein_id
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91 if protein_start:
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92 try:
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93 #TODO Better error handling
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94 amino_acid_original, amino_acid_substituted = variant['amino_acids'].split("/")
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95 substitution = amino_acid_original + str(protein_start) + amino_acid_substituted
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96 if "X" not in substitution:
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97 protein_variants[variant['protein_id']].append(substitution)
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98 consequence += " ," + substitution
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99 except:
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100 pass
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101
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102 output = ""
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103 for key, value in protein_variants.iteritems():
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104 if len(value)>0:
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105 output += "{} {}\n".format(key, (",").join(value))
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106
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107 with open(self.output_file, 'wb') as f:
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108 f.write(output)
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109
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110
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111
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112
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113 if __name__ == "__main__":
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114 parser = argparse.ArgumentParser()
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115 parser.add_argument("--input_file", type=str, required=True, help="Input file location")
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116 parser.add_argument("--output_file", type=str, required=True, help="Output file location")
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117 args = parser.parse_args(sys.argv[1:])
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118 vep = VEPRestClient(args.input_file, args.output_file)
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119 vep.submit()
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120
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