Mercurial > repos > devteam > data_manager_bowtie2_index_builder
changeset 9:47432d88b0a0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 9fa01fe96452d50646e066066b1e556ba4a75ced"
| author | iuc |
|---|---|
| date | Mon, 06 Apr 2020 23:13:03 +0000 |
| parents | 62f1a6310409 |
| children | e816eef8a48f |
| files | data_manager/bowtie2_index_builder.py |
| diffstat | 1 files changed, 26 insertions(+), 26 deletions(-) [+] |
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--- a/data_manager/bowtie2_index_builder.py Sun Dec 22 15:34:40 2019 +0000 +++ b/data_manager/bowtie2_index_builder.py Mon Apr 06 23:13:03 2020 +0000 @@ -11,7 +11,7 @@ DEFAULT_DATA_TABLE_NAMES = ["bowtie2_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: @@ -25,60 +25,60 @@ return sequence_id, sequence_name -def build_bowtie2_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES ): +def build_bowtie2_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES): # 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 = [ 'bowtie2-build', sym_linked_fasta_filename, sequence_id ] + 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 = ['bowtie2-build', sym_linked_fasta_filename, sequence_id] threads = os.environ.get('GALAXY_SLOTS') if threads: args.extend(['--threads', threads]) - proc = subprocess.Popen( args=args, shell=False, cwd=target_directory ) + proc = subprocess.Popen(args=args, shell=False, cwd=target_directory) return_code = proc.wait() if return_code: print("Error building index.", file=sys.stderr) - sys.exit( return_code ) - data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=sequence_id ) + sys.exit(return_code) + data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=sequence_id) for data_table_name in data_table_names: - _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) + _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='append', type="string", default=None, help='data_table_name' ) + 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='append', type="string", default=None, help='data_table_name') (options, args) = parser.parse_args() filename = args[0] - params = loads( open( filename ).read() ) - target_directory = params[ 'output_data' ][0]['extra_files_path'] - os.mkdir( target_directory ) + params = loads(open(filename).read()) + 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_bowtie2_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES ) + build_bowtie2_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES) # save info to json file with open(filename, 'w') as json_out: - json_out.write( dumps( data_manager_dict, sort_keys=True ) ) + json_out.write(dumps(data_manager_dict, sort_keys=True)) if __name__ == "__main__":