Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
comparison data_manager/salmon_index_builder.py @ 4:ef2031036f47 draft
Uploaded
| author | ieguinoa |
|---|---|
| date | Mon, 26 Nov 2018 10:53:58 -0500 |
| parents | f7d9182bdcab |
| children | 3888ec1918d0 |
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| 3:3d12fd3b7cae | 4:ef2031036f47 |
|---|---|
| 32 os.mkdir( target_directory ) | 32 os.mkdir( target_directory ) |
| 33 args = [ 'salmon', 'index' ] | 33 args = [ 'salmon', 'index' ] |
| 34 if options.kmer_size != '': | 34 if options.kmer_size != '': |
| 35 args.append('-k') | 35 args.append('-k') |
| 36 args.append(options.kmer_size) | 36 args.append(options.kmer_size) |
| 37 args.extend( [ '-t' , options.fasta_filename, '-i', sequence_id ] ) | 37 args.extend( [ '-t' , options.fasta_filename, '-i', target_directory ] ) |
| 38 proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) | 38 proc = subprocess.Popen( args=args, shell=False) |
| 39 return_code = proc.wait() | 39 return_code = proc.wait() |
| 40 if return_code: | 40 if return_code: |
| 41 print("Error building index.", file=sys.stderr) | 41 print("Error building index.", file=sys.stderr) |
| 42 sys.exit( return_code ) | 42 sys.exit( return_code ) |
| 43 data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id ) | 43 data_table_entry = dict( value=sequence_id, dbkey=options.fasta_dbkey, name=sequence_name, path=sequence_id ) |
| 69 | 69 |
| 70 if options.fasta_dbkey in [ None, '', '?' ]: | 70 if options.fasta_dbkey in [ None, '', '?' ]: |
| 71 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) ) | 71 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) ) |
| 72 | 72 |
| 73 sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description ) | 73 sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description ) |
| 74 | |
| 75 # build the index | 74 # build the index |
| 76 build_salmon_index( data_manager_dict, options, params, sequence_id, sequence_name ) | 75 build_salmon_index( data_manager_dict, options, params, sequence_id, sequence_name ) |
| 77 | 76 |
| 78 # save info to json file | 77 # save info to json file |
| 79 open( filename, 'w' ).write( dumps( data_manager_dict ) ) | 78 open( filename, 'w' ).write( dumps( data_manager_dict ) ) |