comparison data_manager/picard_index_builder.py @ 3:ae080ff506fd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"

2:b99040168706

from json import dumps, loads

DEFAULT_DATA_TABLE_NAME = "picard_indexes"


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:
        sequence_id = dbkey

        if not sequence_name:
            sequence_name = dbkey
    return sequence_id, sequence_name


def build_picard_index( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ):
    # TODO: allow multiple FASTA input files
    fasta_base_name = os.path.split( fasta_filename )[-1]
    prefix = os.path.splitext( fasta_base_name )[0]
    sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
    os.symlink( fasta_filename, sym_linked_fasta_filename )
    args = [ 'picard', 'CreateSequenceDictionary', 'R=%s' % sym_linked_fasta_filename, 'O=%s.dict' % prefix ]
    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=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 )
    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' )
    (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 )
    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 ) )

    sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )

    # build the index
    build_picard_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 )

    # save info to json file
    open( filename, 'wb' ).write( dumps( data_manager_dict ) )


if __name__ == "__main__":
    main()

3:ae080ff506fd

from json import dumps, loads

DEFAULT_DATA_TABLE_NAME = "picard_indexes"


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:
        sequence_id = dbkey

        if not sequence_name:
            sequence_name = dbkey
    return sequence_id, sequence_name


def build_picard_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME):
    # TODO: allow multiple FASTA input files
    fasta_base_name = os.path.split(fasta_filename)[-1]
    prefix = os.path.splitext(fasta_base_name)[0]
    sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
    os.symlink(fasta_filename, sym_linked_fasta_filename)
    args = ['picard', 'CreateSequenceDictionary', 'R=%s' % sym_linked_fasta_filename, 'O=%s.dict' % prefix]
    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=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)
    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')
    (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)
    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))

    sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)

    # build the index
    build_picard_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)

    # save info to json file
    open(filename, 'w').write(dumps(data_manager_dict, sort_keys=True))


if __name__ == "__main__":
    main()