Mercurial > repos > fubar > data_manager_rnasta

annotate data_manager/rnastar_index_builder.py @ 4:102bdfdda10b draft

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author fubar
date Thu, 08 Jan 2015 17:53:14 -0500
parents 8a2d16bfdae2
children 503097df1670
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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 json import loads, dumps
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13
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14 DEFAULT_DATA_TABLE_NAME = "rnastar_index"
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15 CHUNK_SIZE = 2**20
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17 def get_id_name( params, dbkey, fasta_description=None):
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18 #TODO: ensure sequence_id is unique and does not already appear in location file
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19 sequence_id = params['param_dict']['sequence_id']
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20 if not sequence_id:
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21 sequence_id = dbkey
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22
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23 sequence_name = params['param_dict']['sequence_name']
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24 if not sequence_name:
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25 sequence_name = fasta_description
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26 if not sequence_name:
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27 sequence_name = dbkey
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28 return sequence_id, sequence_name
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31 def _run_command( command, target_directory ):
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32 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar_index_builder-stderr" )
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33 return_code = subprocess.call( command, shell=False, stdout=sys.stdout, stderr=tmp_stderr.fileno() )
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34 if return_code:
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35 tmp_stderr.flush()
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36 tmp_stderr.seek( 0 )
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37 sys.stderr.write( "### star reports an error:\n" )
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38 while True:
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39 chunk = tmp_stderr.read( CHUNK_SIZE )
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40 if not chunk:
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41 break
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42 sys.stderr.write( chunk )
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43 sys.exit( return_code )
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44 tmp_stderr.close()
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45 return return_code
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46
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47
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48 def build_rnastar_index( data_manager_dict, fasta_filename, target_directory,
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49 dbkey, sequence_id, sequence_name, data_table_name,
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50 sjdbOverhang,sjdbGTFfile, sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript,sjdbGTFfeatureExon,sjdbGTFchrPrefix,n_threads):
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51 #TODO: allow multiple FASTA input files
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52 fasta_base_name = os.path.basename( fasta_filename )
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53 #sym_linked_fasta_filename = os.path.join( tmp_dir, fasta_base_name )
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54 #os.symlink( fasta_filename, sym_linked_fasta_filename )
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55 #print >> sys.stdout,'made',sym_linked_fasta_filename
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56 cl = ['STAR','--runMode', 'genomeGenerate', '--genomeFastaFiles', fasta_filename, '--genomeDir', target_directory, '--runThreadN',n_threads ]
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57
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58 if sjdbGTFfile:
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59 cl += [ '--sjdbGTFfeatureExon', sjdbGTFfeatureExon,'--sjdbGTFtagExonParentTranscript',sjdbGTFtagExonParentTranscript]
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60 if (sjdbGTFchrPrefix > ''):
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61 cl += ['--sjdbGTFchrPrefix', sjdbGTFchrPrefix]
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62 cl += ['--sjdbOverhang', sjdbOverhang, '--sjdbGTFfile', sjdbGTFfile]
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63 elif sjdbFileChrStartEnd:
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64 cl += ['--sjdbFileChrStartEnd', sjdbFileChrStartEnd, '--sjdbOverhang', sjdbOverhang]
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65 return_code = _run_command(command=cl,target_directory=target_directory)
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66 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
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67 data_manager_dict.setdefault('data_tables',{})
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68 data_manager_dict['data_tables'].setdefault(data_table_name,[])
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69 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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70 return data_manager_dict
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71
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72
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73 def main():
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74 #Parse Command Line
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75 parser = optparse.OptionParser()
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76 parser.add_option( '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
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77 parser.add_option( '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
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78 parser.add_option( '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
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79 parser.add_option( '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' )
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80 parser.add_option( '--sjdbGTFfile', type="string", default=None )
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81 parser.add_option( '--sjdbGTFchrPrefix', type="string", default=None )
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82 parser.add_option( '--sjdbGTFfeatureExon', type="string", default=None )
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83 parser.add_option( '--sjdbGTFtagExonParentTranscript', type="string", default=None )
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84 parser.add_option( '--sjdbFileChrStartEnd', type="string", default=None )
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85 parser.add_option( '--sjdbOverhang', type="string", default='100' )
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86 parser.add_option( '--runThreadN', type="string", default='4' )
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87 (options, args) = parser.parse_args()
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88 filename = args[0]
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89 # this is passed as an positional parameter in the original wrapper with the extra_files_path from the params
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90 params = loads( open( filename ).read() )
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91 target_directory = params[ 'output_data' ][0]['extra_files_path'].encode('ascii','replace')
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92 try:
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93 os.mkdir( target_directory )
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94 except OSError:
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95 pass
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96
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97 data_manager_dict = {}
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98
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99 dbkey = options.fasta_dbkey
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100
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101 if dbkey in [ None, '', '?' ]:
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102 raise Exception( 'dbkey "%s" does not specify any locally known genome to be indexed.' % ( dbkey ) )
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103
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104 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
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105
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106 #build the index
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107 data_manager_dict = build_rnastar_index( data_manager_dict = data_manager_dict, fasta_filename = options.fasta_filename, target_directory = target_directory,
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108 dbkey = dbkey, sequence_id = sequence_id, sequence_name = sequence_name, data_table_name=options.data_table_name,
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109 sjdbOverhang=options.sjdbOverhang,sjdbGTFfile=options.sjdbGTFfile,
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110 sjdbFileChrStartEnd=options.sjdbFileChrStartEnd,sjdbGTFtagExonParentTranscript=options.sjdbGTFtagExonParentTranscript,
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111 sjdbGTFfeatureExon=options.sjdbGTFfeatureExon,sjdbGTFchrPrefix=options.sjdbGTFchrPrefix,
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112 n_threads=options.runThreadN )
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113
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114
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115 #save info to json file
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116 open( filename, 'wb' ).write( dumps( data_manager_dict ) )
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118 if __name__ == "__main__": main()