comparison dgidb_annotator.py @ 1:8cc7cf4bd833 draft

Uploaded

0:8c6dc9da6c89

'''
Annotates a tabular file with information from the Drug-Gene Interaction (DGI) database.
'''

import optparse, json, urllib2, sys

def __main__():
    # -- Parse command line. --
    parser = optparse.OptionParser()
    parser.add_option('-g', '--gene-name-col', dest='gene_name_col', help='column of gene names')

    # Get gene list.
    gene_list = []
    lines = []
    for line in input_file:
        gene_list.append( line.split('\t')[gene_name_col].strip() )
        lines.append(line.strip())
    
    # Query for results.
    query_str = 'http://dgidb.genome.wustl.edu/api/v1/interactions.json?genes=%s' % ','.join(set(gene_list))
    if options.expert_curated:
        query_str += '&source_trust_levels=Expert%20curated'
    results = urllib2.urlopen(query_str).read()
    results_dict = json.loads(results)
    
    # Process results.
    matched_results = results_dict['matchedTerms']

1:8cc7cf4bd833

'''
Annotates a tabular file with information from the Drug-Gene Interaction (DGI) database.
'''

import optparse, json, urllib2, sys, re

def __main__():
    # -- Parse command line. --
    parser = optparse.OptionParser()
    parser.add_option('-g', '--gene-name-col', dest='gene_name_col', help='column of gene names')

    # Get gene list.
    gene_list = []
    lines = []
    for line in input_file:
        entry = line.split('\t')[gene_name_col].strip()
        # Some annotations may be of the form 
        #    <gene_name>(<splicing_info>) or <gene_name>;<gene_name>(splicing_info)
        gene_list.append(entry.split(';')[0].split('(')[0])
        lines.append(line.strip())
    
    # Query for results.
    query_str = 'http://dgidb.genome.wustl.edu/api/v1/interactions.json?genes=%s' % ','.join(set(gene_list))
    if options.expert_curated:
        query_str += '&source_trust_levels=Expert%20curated'
    print query_str
    results = urllib2.urlopen(query_str).read()
    results_dict = json.loads(results)
    
    # Process results.
    matched_results = results_dict['matchedTerms']