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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 tempfile
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6 import optparse
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7 import subprocess
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8
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9 from galaxy.util.json import from_json_string, to_json_string
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10
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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 = "bowtie_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_bowtie_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME, color_space = False ):
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30 #TODO: allow multiple FASTA input files
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31 #tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-bowtie-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 args = [ 'bowtie-build' ]
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36 if color_space:
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37 args.append( '-c' )
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38 args.append( sym_linked_fasta_filename)
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39 args.append( fasta_base_name )
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40 args.append( sym_linked_fasta_filename )
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41 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-bowtie-index-builder-stderr" )
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42 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
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43 return_code = proc.wait()
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44 if return_code:
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45 tmp_stderr.flush()
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46 tmp_stderr.seek(0)
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47 print >> sys.stderr, "Error building index:"
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48 while True:
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49 chunk = tmp_stderr.read( CHUNK_SIZE )
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50 if not chunk:
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51 break
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52 sys.stderr.write( chunk )
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53 sys.exit( return_code )
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54 tmp_stderr.close()
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55 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
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56 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
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57
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58 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
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59 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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60 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
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61 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
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62 return data_manager_dict
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63
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64 def main():
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65 #Parse Command Line
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66 parser = optparse.OptionParser()
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67 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
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68 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
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69 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
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70 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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71 parser.add_option( '-c', '--color_space', dest='color_space', action='store_true', default=False, help='color_space' )
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72 (options, args) = parser.parse_args()
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73
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74 filename = args[0]
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75
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76 params = from_json_string( open( filename ).read() )
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77 target_directory = params[ 'output_data' ][0]['extra_files_path']
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78 os.mkdir( target_directory )
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79 data_manager_dict = {}
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80
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81 dbkey = options.fasta_dbkey
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82
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83 if dbkey in [ None, '', '?' ]:
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84 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
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85
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86 sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
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87
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88 #build the index
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89 build_bowtie_index( 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, color_space=options.color_space )
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90
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91 #save info to json file
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92 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
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93
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94 if __name__ == "__main__": main()
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