Mercurial > repos > in_silico > cravat_annotate_mutations

comparison cravat_annotate/cravat_annotate.py @ 22:e05043fbb945 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author in_silico
date Wed, 27 Jun 2018 17:53:25 -0400
parents
children
comparison
equal deleted inserted replaced
21:94fdd28c0dbb 22:e05043fbb945
1 """
2 A galaxy wrapper for the /rest/service/query API endpoint on Cravat.
3 """
4
5
6 import requests
7 import json
8 import sys
9 import re
10 import argparse
11 import ipdb
12
13
14 # The endpoint that CravatQuerys are submitted to
15 endpoint = 'http://www.cravat.us/CRAVAT/rest/service/query'
16
17
18 # The value delimiter used in the Cravat input file to delimit values
19 delimiter = "\t"
20
21
22 # Defualt indices for intepretting a cravat file's row of data in to a CravatQuery
23 cr_mapping = {
24 'chromosome': 1,
25 'position': 2,
26 'strand': 3,
27 'reference': 4,
28 'alternate': 5
29 }
30
31
32 # The neccessary attributes neeeded to submit a query.
33 query_keys = [
34 'chromosome', 'position', 'strand', 'reference', 'alternate'
35 ]
36
37
38 # Expected response keys from server. Ordered in list so that galaxy output has uniform column ordering run-to-run.
39 # If cravat server returns additional keys, they are appended to and included in output.
40 response_keys = [
41 "Chromosome", "Position", "Strand", "Reference base(s)", "Alternate base(s)",
42 "HUGO symbol", "S.O. transcript", "Sequence ontology protein change", "Sequence ontology",
43 "S.O. all transcripts", "gnomAD AF", "gnomAD AF (African)", "gnomAD AF (Amrican)",
44 "gnomAD AF (Ashkenazi Jewish)", "gnomAD AF (East Asian)", "gnomAD AF (Finnish)",
45 "gnomAD AF (Non-Finnish European)", "gnomAD AF (Other)", "gnomAD AF (South Asian)",
46 "1000 Genomes AF", "ESP6500 AF (average)", "ESP6500 AF (European American)",
47 "ESP6500 AF (African American)", "COSMIC transcript", "COSMIC protein change",
48 "COSMIC variant count [exact nucleotide change]", "cosmic_site_nt", "CGL driver class",
49 "TARGET", "dbSNP", "cgc_role", "cgc_inheritance", "cgc_tumor_type_somatic",
50 "cgc_tumor_type_germline", "ClinVar", "ClinVar disease identifier", "ClinVar XRef",
51 "GWAS Phenotype (GRASP)", "GWAS PMID (GRASP)", "Protein 3D variant"
52 ]
53
54
55 def get_args():
56 parser = argparse.ArgumentParser()
57 parser.add_argument('--input',
58 '-i',
59 required = True,
60 help='Input path to a cravat file for querying',)
61 parser.add_argument('--output',
62 '-o',
63 default = None,
64 help = 'Output path to write results from query')
65 return parser.parse_args()
66
67
68 def format_chromosome(chrom):
69 """ : Ensure chromosome entry is propely formatted for use as querying attribute. """
70 if chrom[0:3] == 'chr':
71 return chrom
72 return 'chr' + str(chrom)
73
74
75 def get_query_string(row):
76 """ : From a row dict, return a query string for the Cravat server.
77 : The row dict is cravat headeres associated to their values of that row.
78 """
79 return '_'.join([ row['chromosome'], row['position'], row['strand'], row['reference'], row['alternate'] ])
80
81
82 def query(in_path, out_path):
83 """ : From a Cravat the file at in_path, query each line on the Cravat server.
84 : Write the response values to file at out_path.
85 """
86
87 with open(in_path, 'r') as in_file, \
88 open(out_path, 'w') as out_file:
89
90 for line in in_file:
91 line = line.strip().split('\t')
92 # row is dict of cravat col headers assioted values in this line
93 row = { header: line[index] for header, index in cr_mapping.items() }
94 row['chromosome'] = format_chromosome(row['chromosome'])
95 query_string = get_query_string(row)
96 call = requests.get(endpoint, params={ 'mutation': query_string })
97 if call.status_code != 200 or call.text == "":
98 raise requests.RequestException("Bad Server Response. Respone code: '{}', Response Text: '{}'".format(call.status_code, call.text))
99 json_response = json.loads(call.text)
100 # See if server returned additional json key-val paris not expected in response_keys
101 for key in json_response:
102 if key not in response_keys:
103 response_keys.append(key)
104 # Write key in order of response_keys to standardize order of output columns
105 wrote = False
106 for key in response_keys:
107 if key not in json_response:
108 val = None
109 val = json_response[key]
110 # Format standardization for numerics
111 try:
112 val = float(val)
113 val = format(val, ".4f")
114 except:
115 pass
116 if wrote:
117 out_file.write("\t")
118 out_file.write(val)
119 wrote = True
120 out_file.write("\n")
121
122
123 if __name__ == "__main__":
124 cli_args = get_args()
125 if cli_args.output == None:
126 base, _ = os.path.split(cli_args.input)
127 cli_args.output = os.path.join(base, "cravat_converted.txt")
128 query(cli_args.input, cli_args.output)