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1 import requests
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2 import json
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3 import sys
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4 import re
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5 import argparse
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6 from __future__ import print_function
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7
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8
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9 # The endpoint that CravatQuerys are submitted to
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10 endpoint = 'http://www.cravat.us/CRAVAT/rest/service/query'
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11
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12
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13 # newline and delimiter values used in the output file
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14 delimiter = "\t"
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15 newline = "\n"
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16
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17
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18 # Defualt indices for intepretting a cravat file's row of data in to a CravatQuery
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19 cr_mapping = {
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20 'chromosome': 1,
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21 'position': 2,
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22 'strand': 3,
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23 'reference': 4,
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24 'alternate': 5
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25 }
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26
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27
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28 # The neccessary attributes neeeded to submit a query.
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29 query_keys = [
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30 'chromosome', 'position', 'strand', 'reference', 'alternate'
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31 ]
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32
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33
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34 # Expected response keys from server. Ordered in list so that galaxy output has uniform column ordering run-to-run.
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35 # If cravat server returns additional keys, they are appended to and included in output.
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36 ordered_keys = [
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37 "Chromosome", "Position", "Strand", "Reference base(s)", "Alternate base(s)",
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38 "HUGO symbol", "S.O. transcript", "Sequence ontology protein change", "Sequence ontology",
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39 "S.O. all transcripts", "gnomAD AF", "gnomAD AF (African)", "gnomAD AF (Amrican)",
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40 "gnomAD AF (Ashkenazi Jewish)", "gnomAD AF (East Asian)", "gnomAD AF (Finnish)",
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41 "gnomAD AF (Non-Finnish European)", "gnomAD AF (Other)", "gnomAD AF (South Asian)",
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42 "1000 Genomes AF", "ESP6500 AF (average)", "ESP6500 AF (European American)",
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43 "ESP6500 AF (African American)", "COSMIC transcript", "COSMIC protein change",
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44 "COSMIC variant count [exact nucleotide change]", "cosmic_site_nt", "CGL driver class",
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45 "TARGET", "dbSNP", "cgc_role", "cgc_inheritance", "cgc_tumor_type_somatic",
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46 "cgc_tumor_type_germline", "ClinVar", "ClinVar disease identifier", "ClinVar XRef",
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47 "GWAS Phenotype (GRASP)", "GWAS PMID (GRASP)", "Protein 3D variant"
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48 ]
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49
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50
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51 def get_args():
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52 parser = argparse.ArgumentParser()
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53 parser.add_argument('--input',
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54 '-i',
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55 required = True,
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56 help='Input path to a cravat file for querying',)
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57 parser.add_argument('--output',
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58 '-o',
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59 default = None,
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60 help = 'Output path to write results from query')
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61 return parser.parse_args()
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62
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63
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64 def format_chromosome(chrom):
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65 """ : Ensure chromosome entry is propely formatted for use as querying attribute. """
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66 if chrom[0:3] == 'chr':
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67 return chrom
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68 return 'chr' + str(chrom)
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69
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70
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71 def get_query_string(row):
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72 """ : From a row dict, return a query string for the Cravat server.
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73 : The row dict is cravat headeres associated to their values of that row.
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74 """
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75 return '_'.join([ row['chromosome'], row['position'], row['strand'], row['reference'], row['alternate'] ])
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76
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77
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78 def query(in_path, out_path):
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79 """ : From a Cravat the file at in_path, query each line on the Cravat server.
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80 : Write the response values to file at out_path.
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81 """
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82 with open(in_path, 'r') as in_file, \
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83 open(out_path, 'w') as out_file:
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84 for line in in_file:
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85 try:
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86 line = line.strip().split('\t')
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87 # row is dict of cravat col headers assioted values in this line
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88 row = { header: line[index] for header, index in cr_mapping.items() }
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89 row['chromosome'] = format_chromosome(row['chromosome'])
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90 query_string = get_query_string(row)
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91 call = requests.get(endpoint, params={ 'mutation': query_string })
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92 if call.status_code != 200 or call.text == "":
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93 raise requests.RequestException('Bad server response for query="{}". Respone code: "{}", Response Text: "{}"'
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94 .format(query_string, call.status_code, call.text))
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95 json_response = json.loads(call.text)
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96 # See if server returned additional json key-vals not expected in ordered_keys
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97 for key in json_response:
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98 if key not in ordered_keys:
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99 ordered_keys.append(key)
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100 # Write key in order of ordered_keys to standardize order of output columns
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101 wrote = False
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102 for key in ordered_keys:
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103 if key in json_response:
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104 val = json_response[key]
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105 else:
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106 val = None
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107 # Standardize format for numeric values
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108 try:
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109 val = float(val)
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110 val = format(val, ".4f")
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111 except:
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112 pass
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113 if wrote:
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114 out_file.write(delimiter)
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115 out_file.write(str(val))
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116 wrote = True
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117 out_file.write(newline)
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118 except Exception as e:
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119 print(e, file=sys.stderr)
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120 continue
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121
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122
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123 if __name__ == "__main__":
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124 cli_args = get_args()
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125 if cli_args.output == None:
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126 base, _ = os.path.split(cli_args.input)
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127 cli_args.output = os.path.join(base, "cravat_converted.txt")
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128 query(cli_args.input, cli_args.output)
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