Mercurial > repos > fubar > data_manager_rnasta
annotate data_manager/rnastar_index_builder.py @ 5:503097df1670 draft
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| author | fubar |
|---|---|
| date | Fri, 09 Jan 2015 22:38:21 -0500 |
| parents | 102bdfdda10b |
| children | f9d8dc8c2152 |
| rev | line source |
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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 |
| 5 | 5 # fixed some stupid bugs January 2015 |
| 6 | |
| 7 | |
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8 import sys |
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9 import os |
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10 import tempfile |
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11 import optparse |
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12 import subprocess |
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13 |
| 5 | 14 from galaxy.util.json import from_json_string, to_json_string |
| 15 | |
| 16 | |
| 17 CHUNK_SIZE = 2**20 | |
| 18 ONE_GB = 2**30 | |
| 19 | |
| 20 # from json import loads, dumps | |
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21 |
| 4 | 22 DEFAULT_DATA_TABLE_NAME = "rnastar_index" |
| 5 | 23 |
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24 |
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25 def get_id_name( params, dbkey, fasta_description=None): |
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26 #TODO: ensure sequence_id is unique and does not already appear in location file |
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27 sequence_id = params['param_dict']['sequence_id'] |
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28 if not sequence_id: |
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29 sequence_id = dbkey |
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30 |
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31 sequence_name = params['param_dict']['sequence_name'] |
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32 if not sequence_name: |
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33 sequence_name = fasta_description |
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34 if not sequence_name: |
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35 sequence_name = dbkey |
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36 return sequence_id, sequence_name |
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37 |
| 4 | 38 |
| 39 def _run_command( command, target_directory ): | |
| 40 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar_index_builder-stderr" ) | |
| 41 return_code = subprocess.call( command, shell=False, stdout=sys.stdout, stderr=tmp_stderr.fileno() ) | |
| 42 if return_code: | |
| 43 tmp_stderr.flush() | |
| 44 tmp_stderr.seek( 0 ) | |
| 45 sys.stderr.write( "### star reports an error:\n" ) | |
| 46 while True: | |
| 47 chunk = tmp_stderr.read( CHUNK_SIZE ) | |
| 48 if not chunk: | |
| 49 break | |
| 50 sys.stderr.write( chunk ) | |
| 51 sys.exit( return_code ) | |
| 52 tmp_stderr.close() | |
| 53 return return_code | |
| 54 | |
| 55 | |
| 56 def build_rnastar_index( data_manager_dict, fasta_filename, target_directory, | |
| 57 dbkey, sequence_id, sequence_name, data_table_name, | |
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58 sjdbOverhang,sjdbGTFfile, sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript,sjdbGTFfeatureExon,sjdbGTFchrPrefix,n_threads): |
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59 #TODO: allow multiple FASTA input files |
| 4 | 60 fasta_base_name = os.path.basename( fasta_filename ) |
| 5 | 61 sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) |
| 62 os.symlink( fasta_filename, sym_linked_fasta_filename ) | |
| 63 print >> sys.stdout,'made',sym_linked_fasta_filename | |
| 64 cl = ['STAR','--runMode', 'genomeGenerate', '--genomeFastaFiles', sym_linked_fasta_filename, '--genomeDir', target_directory, '--runThreadN',n_threads ] | |
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65 |
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66 if sjdbGTFfile: |
| 4 | 67 cl += [ '--sjdbGTFfeatureExon', sjdbGTFfeatureExon,'--sjdbGTFtagExonParentTranscript',sjdbGTFtagExonParentTranscript] |
| 68 if (sjdbGTFchrPrefix > ''): | |
| 69 cl += ['--sjdbGTFchrPrefix', sjdbGTFchrPrefix] | |
| 70 cl += ['--sjdbOverhang', sjdbOverhang, '--sjdbGTFfile', sjdbGTFfile] | |
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71 elif sjdbFileChrStartEnd: |
| 4 | 72 cl += ['--sjdbFileChrStartEnd', sjdbFileChrStartEnd, '--sjdbOverhang', sjdbOverhang] |
| 5 | 73 |
| 74 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar-index-builder-stderr" ) | |
| 75 proc = subprocess.Popen( args=cl, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) | |
| 76 return_code = proc.wait() | |
| 77 if return_code: | |
| 78 tmp_stderr.flush() | |
| 79 tmp_stderr.seek(0) | |
| 80 print >> sys.stderr, "Error building index:" | |
| 81 while True: | |
| 82 chunk = tmp_stderr.read( CHUNK_SIZE ) | |
| 83 if not chunk: | |
| 84 break | |
| 85 sys.stderr.write( chunk ) | |
| 86 sys.exit( return_code ) | |
| 87 tmp_stderr.close() | |
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88 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) |
| 5 | 89 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) |
| 90 | |
| 91 | |
| 92 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): | |
| 93 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) | |
| 94 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) | |
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95 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) |
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96 return data_manager_dict |
| 5 | 97 |
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98 def main(): |
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99 #Parse Command Line |
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100 parser = optparse.OptionParser() |
| 4 | 101 parser.add_option( '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) |
| 102 parser.add_option( '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) | |
| 103 parser.add_option( '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) | |
| 104 parser.add_option( '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) | |
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105 parser.add_option( '--sjdbGTFfile', type="string", default=None ) |
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106 parser.add_option( '--sjdbGTFchrPrefix', type="string", default=None ) |
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107 parser.add_option( '--sjdbGTFfeatureExon', type="string", default=None ) |
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108 parser.add_option( '--sjdbGTFtagExonParentTranscript', type="string", default=None ) |
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109 parser.add_option( '--sjdbFileChrStartEnd', type="string", default=None ) |
| 4 | 110 parser.add_option( '--sjdbOverhang', type="string", default='100' ) |
| 111 parser.add_option( '--runThreadN', type="string", default='4' ) | |
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112 (options, args) = parser.parse_args() |
| 5 | 113 filename = args[0] |
| 114 params = from_json_string( open( filename ).read() ) | |
| 4 | 115 target_directory = params[ 'output_data' ][0]['extra_files_path'].encode('ascii','replace') |
| 5 | 116 data_manager_dict = {} |
| 117 dbkey = options.fasta_dbkey | |
| 118 if dbkey in [ None, '', '?' ]: | |
| 119 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) ) | |
| 120 | |
| 121 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description ) | |
| 122 | |
| 4 | 123 try: |
| 124 os.mkdir( target_directory ) | |
| 125 except OSError: | |
| 126 pass | |
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127 #build the index |
| 5 | 128 build_rnastar_index( data_manager_dict = data_manager_dict, fasta_filename = options.fasta_filename, target_directory = target_directory, |
| 4 | 129 dbkey = dbkey, sequence_id = sequence_id, sequence_name = sequence_name, data_table_name=options.data_table_name, |
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130 sjdbOverhang=options.sjdbOverhang,sjdbGTFfile=options.sjdbGTFfile, |
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131 sjdbFileChrStartEnd=options.sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript=options.sjdbGTFtagExonParentTranscript, |
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132 sjdbGTFfeatureExon=options.sjdbGTFfeatureExon,sjdbGTFchrPrefix=options.sjdbGTFchrPrefix, |
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133 n_threads=options.runThreadN ) |
| 5 | 134 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) ) |
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135 |
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136 if __name__ == "__main__": main() |
| 5 | 137 |