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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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3 # adapted from Dan's BWA one for rna star
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4 # ross lazarus sept 2014
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5 #
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6 import sys
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7 import os
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8 import tempfile
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9 import optparse
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10 import subprocess
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11
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12 from galaxy.util.json import from_json_string, to_json_string
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13
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14 DEFAULT_DATA_TABLE_NAME = "rnastar_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_rnastar_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name,
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30 sjdbOverhang,sjdbGTFfile, sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript,sjdbGTFfeatureExon,sjdbGTFchrPrefix,n_threads):
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31 #TODO: allow multiple FASTA input files
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32 #tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-bwa-index-builder-' )
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33 fasta_base_name = os.path.split( fasta_filename )[-1]
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34 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
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35 os.symlink( fasta_filename, sym_linked_fasta_filename )
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36 pdict={'target_directory':target_directory,'n_threads':n_threads, 'sjdbFileChrStartEnd':sjdbFileChrStartEnd,
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37 'sjdbGTFtagExonParentTranscript':sjdbGTFtagExonParentTranscript, 'sjdbGTFfeatureExon':sjdbGTFfeatureExon,
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38 'sjdbGTFchrPrefix':sjdbGTFchrPrefix,'sjdbOverhang':sjdbOverhang, 'sjdbGTFfile':sjdbGTFfile,
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39 'sym_linked_fasta_filename':sym_linked_fasta_filename}
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40
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41 cl = 'STAR --runMode genomeGenerate --genomeFastaFiles %(sym_linked_fasta_filename)s --genomeDir %(target_directory)s --runThreadN %(n_threads)s' % pdict
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42 if sjdbGTFfile:
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43 cl += '''--sjdbGTFchrPrefix %(sjdbGTFchrPrefix)s --sjdbGTFfeatureExon %(sjdbGTFfeatureExon)s --sjdbOverhang %(sjdbOverhang)s
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44 --sjdbGTFfile %(sjdbGTFfile)s --sjdbGTFtagExonParentTranscript %(sjdbGTFtagExonParentTranscript)s''' % pdict
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45 elif sjdbFileChrStartEnd:
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46 cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' % pdict
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47 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar-index-builder-stderr" )
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48 args = cl.split(' ')
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49 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
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50 return_code = proc.wait()
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51 if return_code:
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52 tmp_stderr.flush()
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53 tmp_stderr.seek(0)
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54 print >> sys.stderr, "Error building index: retcode=",retcode
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55 while True:
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56 chunk = tmp_stderr.read( CHUNK_SIZE )
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57 if not chunk:
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58 break
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59 sys.stderr.write( chunk )
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60 tmp_stderr.close()
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61 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
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62 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
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63
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64 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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65 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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66 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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67 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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68 return data_manager_dict
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69
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70 def main():
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71 #Parse Command Line
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72 parser = optparse.OptionParser()
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73 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
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74 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
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75 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
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76 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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77 parser.add_option( '--out_file', default=None)
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78 parser.add_option( '--out_index_path', default=None)
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79 parser.add_option( '--sjdbGTFfile', type="string", default=None )
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80 parser.add_option( '--sjdbGTFchrPrefix', type="string", default=None )
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81 parser.add_option( '--sjdbGTFfeatureExon', type="string", default=None )
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82 parser.add_option( '--sjdbGTFtagExonParentTranscript', type="string", default=None )
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83 parser.add_option( '--sjdbFileChrStartEnd', type="string", default=None )
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84 parser.add_option( '--sjdbOverhang', type="int", default=100 )
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85 parser.add_option( '--runThreadN', type="int", default=4 )
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86 (options, args) = parser.parse_args()
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87
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88 filename = options.out_file
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89 params = from_json_string( open( filename ).read() )
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90 target_directory = options.out_index_path
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91 os.mkdirs( target_directory )
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92 data_manager_dict = {}
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93
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94 dbkey = options.fasta_dbkey
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95
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96 if dbkey in [ None, '', '?' ]:
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97 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
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98
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99 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
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100
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101 #build the index
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102 build_rnastar_index( data_manager_dict, options.fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name,
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103 sjdbOverhang=options.sjdbOverhang,sjdbGTFfile=options.sjdbGTFfile,
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104 sjdbFileChrStartEnd=options.sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript=options.sjdbGTFtagExonParentTranscript,
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105 sjdbGTFfeatureExon=options.sjdbGTFfeatureExon,sjdbGTFchrPrefix=options.sjdbGTFchrPrefix,
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106 n_threads=options.runThreadN )
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107
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108
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109 #save info to json file
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110 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
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111
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112 if __name__ == "__main__": main()
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