annotate data_manager/data_manager_snpEff_databases.py @ 0:9ac823a8b328 draft

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#!/usr/bin/env python

import sys
import os
import re
import tempfile
import subprocess
import fileinput
import shutil
import optparse
import urllib2
from ftplib import FTP
import tarfile

from galaxy.util.json import from_json_string, to_json_string

def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit(1)

def fetch_databases(data_manager_dict, target_directory, jar_path):
    (snpEff_dir,snpEff_jar) = os.path.split(jar_path)
    if not os.path.exists(target_directory):
        os.makedirs(target_directory)
    databases_path = os.path.join( target_directory, 'databases.out' )
    databases_output = open(databases_path,'w')
    args = [ 'java','-jar', ]
    args.append( snpEff_jar )
    args.append( 'databases' )
    # tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-snpEff-stderr" )
    # databases_output = open(databases_path)
    # proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno(), stderr=tmp_stderr.fileno() )
    proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() )
    return_code = proc.wait()
    if return_code:
        sys.exit( return_code )
    databases_output.close()
    try:
        data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
        data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] )
        data_table_entries = []
        fh = open(databases_path,'r')
        for i,line in enumerate(fh):
            fields = line.split('\t')
            if len(fields) >= 2:
                genome_version = fields[0].strip()
                if genome_version.startswith("Genome") or genome_version.startswith("-"):
                    continue
                #snpeff test genome
                if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
                    continue
                description = fields[1].strip() + ' : ' + genome_version
                data_table_entries.append(dict(value=genome_version, name=description))
        data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries
    except Exception, e:
        stop_err( 'Error parsing %s %s\n' % (config,str( e )) )
    else:
        fh.close()
    return data_manager_dict

def main():
    #Parse Command Line
    parser = optparse.OptionParser()
    parser.add_option( '-j', '--jar_path', dest='jar_path', action='store', type="string", default=None, help='snpEff.jar path' )
    (options, args) = parser.parse_args()

    filename = args[0]

    params = from_json_string( open( filename ).read() )
    target_directory = params[ 'output_data' ][0]['extra_files_path']
    os.mkdir( target_directory )
    data_manager_dict = {}


    #Create Defuse Reference Data
    data_manager_dict = fetch_databases( data_manager_dict, target_directory, options.jar_path)

    #save info to json file
    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )

if __name__ == "__main__": main()