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1 #!/usr/bin/env python
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2 #Jim Johnson
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3
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4 import sys
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5 import os
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6 import tempfile
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7 import optparse
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8 import subprocess
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9
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10 from galaxy.util.json import from_json_string, to_json_string
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11
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12 CHUNK_SIZE = 2**20
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13
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14 DEFAULT_DATA_TABLE_NAME = "picard_indexes"
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15
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16 def get_id_name( params, dbkey, fasta_description=None):
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17 #TODO: ensure sequence_id is unique and does not already appear in location file
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18 sequence_id = params['param_dict']['sequence_id']
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19 if not sequence_id:
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20 sequence_id = dbkey
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21
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22 sequence_name = params['param_dict']['sequence_name']
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23 if not sequence_name:
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24 sequence_name = fasta_description
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25 if not sequence_name:
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26 sequence_name = dbkey
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27 return sequence_id, sequence_name
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28
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29 def build_picard_index( jar_path, data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME):
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30 #TODO: allow multiple FASTA input files
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31 #tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-picard-index-builder-' )
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32 fasta_base_name = os.path.split( fasta_filename )[-1]
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33 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
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34 os.symlink( fasta_filename, sym_linked_fasta_filename )
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35 basename,ext = os.path.splitext(fasta_base_name)
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36 ref_dict = "%s.dict" % basename
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37 args = [ 'java','-Xmx4G','-jar', jar_path, "R=%s" % sym_linked_fasta_filename, "O=%s" % ref_dict ]
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38 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-picard-index-builder-stderr" )
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39 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
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40 return_code = proc.wait()
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41 if return_code:
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42 tmp_stderr.flush()
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43 tmp_stderr.seek(0)
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44 print >> sys.stderr, "Error building index:"
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45 while True:
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46 chunk = tmp_stderr.read( CHUNK_SIZE )
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47 if not chunk:
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48 break
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49 sys.stderr.write( chunk )
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50 sys.exit( return_code )
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51 tmp_stderr.close()
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52 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
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53 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
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54
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55 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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56 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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57 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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58 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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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( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
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65 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
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66 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
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67 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' )
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68 parser.add_option( '-j', '--jar_path', dest='jar_path', action='store', type="string", default=None, help='path to CreateSequenceDictionary.jar' )
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69 (options, args) = parser.parse_args()
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70
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71 filename = args[0]
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72
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73 params = from_json_string( open( filename ).read() )
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74 target_directory = params[ 'output_data' ][0]['extra_files_path']
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75 os.mkdir( target_directory )
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76 data_manager_dict = {}
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77
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78 dbkey = options.fasta_dbkey
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79
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80 if dbkey in [ None, '', '?' ]:
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81 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
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82
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83 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
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84
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85 #build the index
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86 build_picard_index( options.jar_path, data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME )
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87
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88 #save info to json file
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89 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
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90
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91 if __name__ == "__main__": main()
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