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1 #!/usr/bin/env python
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2
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3 import sys
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4 import os
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5 import re
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6 import tempfile
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7 import subprocess
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8 import fileinput
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9 import shutil
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10 import optparse
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11 import urllib2
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12 from ftplib import FTP
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13 import tarfile
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14
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15 from galaxy.util.json import from_json_string, to_json_string
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16
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17 def stop_err(msg):
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18 sys.stderr.write(msg)
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19 sys.exit(1)
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20
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21 def fetch_databases(data_manager_dict, target_directory, jar_path):
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22 (snpEff_dir,snpEff_jar) = os.path.split(jar_path)
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23 if not os.path.exists(target_directory):
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24 os.makedirs(target_directory)
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25 databases_path = os.path.join( target_directory, 'databases.out' )
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26 databases_output = open(databases_path,'w')
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27 args = [ 'java','-jar', ]
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28 args.append( snpEff_jar )
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29 args.append( 'databases' )
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30 # tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-snpEff-stderr" )
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31 # databases_output = open(databases_path)
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32 # proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno(), stderr=tmp_stderr.fileno() )
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33 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() )
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34 return_code = proc.wait()
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35 if return_code:
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36 sys.exit( return_code )
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37 databases_output.close()
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38 try:
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39 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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6
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40 data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] )
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41 data_table_entries = []
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42 fh = open(databases_path,'r')
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43 for i,line in enumerate(fh):
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44 fields = line.split('\t')
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45 if len(fields) >= 2:
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46 genome_version = fields[0].strip()
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47 if genome_version.startswith("Genome") or genome_version.startswith("-"):
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48 continue
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49 #snpeff test genome
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50 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'):
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51 continue
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52 description = fields[1].strip() + ' : ' + genome_version
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53 data_table_entries.append(dict(value=genome_version, name=description))
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54 data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries
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55 except Exception, e:
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56 stop_err( 'Error parsing %s %s\n' % (config,str( e )) )
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57 else:
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58 fh.close()
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59 return data_manager_dict
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60
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61 def main():
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62 #Parse Command Line
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63 parser = optparse.OptionParser()
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64 parser.add_option( '-j', '--jar_path', dest='jar_path', action='store', type="string", default=None, help='snpEff.jar path' )
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65 (options, args) = parser.parse_args()
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66
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67 filename = args[0]
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68
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69 params = from_json_string( open( filename ).read() )
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70 target_directory = params[ 'output_data' ][0]['extra_files_path']
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71 os.mkdir( target_directory )
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72 data_manager_dict = {}
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73
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74
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75 #Create Defuse Reference Data
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76 data_manager_dict = fetch_databases( data_manager_dict, target_directory, options.jar_path)
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77
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78 #save info to json file
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79 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
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80
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81 if __name__ == "__main__": main()
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82
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