Mercurial > repos > iuc > data_manager_bowtie_index_builder
changeset 5:08a3583826fa draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie_index_builder commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
| author | iuc |
|---|---|
| date | Sun, 22 Nov 2020 12:44:59 +0000 |
| parents | 86e9af693a33 |
| children | cb157f55b4fd |
| files | data_manager/bowtie_index_builder.py |
| diffstat | 1 files changed, 36 insertions(+), 34 deletions(-) [+] |
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--- a/data_manager/bowtie_index_builder.py Fri Jun 09 06:12:02 2017 -0400 +++ b/data_manager/bowtie_index_builder.py Sun Nov 22 12:44:59 2020 +0000 @@ -13,7 +13,7 @@ DEFAULT_DATA_TABLE_NAME = "bowtie_indexes" -def get_id_name( params, dbkey, fasta_description=None): +def get_id_name(params, dbkey, fasta_description=None): # TODO: ensure sequence_id is unique and does not already appear in location file sequence_id = params['param_dict']['sequence_id'] if not sequence_id: @@ -27,70 +27,72 @@ return sequence_id, sequence_name -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 ): +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): # TODO: allow multiple FASTA input files - fasta_base_name = os.path.split( fasta_filename )[-1] - sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name ) - os.symlink( fasta_filename, sym_linked_fasta_filename ) - args = [ 'bowtie-build' ] + fasta_base_name = os.path.split(fasta_filename)[-1] + sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name) + os.symlink(fasta_filename, sym_linked_fasta_filename) + args = ['bowtie-build'] if color_space: - args.append( '-C' ) - args.append( sym_linked_fasta_filename) - args.append( fasta_base_name ) - args.append( sym_linked_fasta_filename ) - tmp_stderr = tempfile.NamedTemporaryFile( prefix="tmp-data-manager-bowtie-index-builder-stderr" ) - proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) + args.append('-C') + args.append(sym_linked_fasta_filename) + args.append(fasta_base_name) + args.append(sym_linked_fasta_filename) + tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-bowtie-index-builder-stderr") + proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno()) return_code = proc.wait() if return_code: tmp_stderr.flush() tmp_stderr.seek(0) print("Error building index:", file=sys.stderr) while True: - chunk = tmp_stderr.read( CHUNK_SIZE ) + chunk = tmp_stderr.read(CHUNK_SIZE) if not chunk: break - sys.stderr.write( chunk ) - sys.exit( return_code ) + sys.stderr.write(chunk) + sys.exit(return_code) tmp_stderr.close() - data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) - _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) + data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name) + _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry) -def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): - data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) - data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) - data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) +def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry): + data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {}) + data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get(data_table_name, []) + data_manager_dict['data_tables'][data_table_name].append(data_table_entry) return data_manager_dict def main(): parser = optparse.OptionParser() - parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) - parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) - parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) - parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) - parser.add_option( '-c', '--color_space', dest='color_space', action='store_true', default=False, help='color_space' ) + parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename') + parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey') + parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description') + parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name') + parser.add_option('-c', '--color_space', dest='color_space', action='store_true', default=False, help='color_space') (options, args) = parser.parse_args() filename = args[0] - params = json.loads( open( filename ).read() ) - target_directory = params[ 'output_data' ][0]['extra_files_path'] - os.mkdir( target_directory ) + with open(filename) as fh: + params = json.load(fh) + target_directory = params['output_data'][0]['extra_files_path'] + os.mkdir(target_directory) data_manager_dict = {} dbkey = options.fasta_dbkey - if dbkey in [ None, '', '?' ]: - raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) ) + if dbkey in [None, '', '?']: + raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey)) - sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description ) + sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description) # build the index - 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 ) + 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) # save info to json file - open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) + with open(filename, 'w') as fh: + json.dump(data_manager_dict, fh, sort_keys=True) if __name__ == "__main__":