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