def __gather_contigset(resource_file_extension, input_files, output_file, new_resource_file=None, skip_empty=True): """ :param input_files: List of file paths :param output_file: File Path :param new_resource_file: the path of the file to which the other contig files are consolidated :param skip_empty: Ignore empty files (doesn't do much yet) :return: Output file :rtype: str """ if skip_empty: _input_files = [] for file_name in input_files: cs = ContigSet(file_name) if len(cs.toExternalFiles()) > 0: _input_files.append(file_name) input_files = _input_files tbr = ContigSet(*input_files) if not new_resource_file: if output_file.endswith('xml'): new_resource_file = output_file[:-3] + resource_file_extension tbr.consolidate(new_resource_file) tbr.newUuid() tbr.write(output_file) return output_file
def __gather_contigset(resource_file_extension, input_files, output_file, new_resource_file=None, skip_empty=True): """ :param input_files: List of file paths :param output_file: File Path :param new_resource_file: the path of the file to which the other contig files are consolidated :param skip_empty: Ignore empty files (doesn't do much yet) :return: Output file :rtype: str """ if skip_empty: _input_files = [] for file_name in input_files: cs = ContigSet(file_name) if len(cs.toExternalFiles()) > 0: _input_files.append(file_name) input_files = _input_files tbr = ContigSet(*input_files) if not new_resource_file: if output_file.endswith('xml'): new_resource_file = output_file[:-3] + resource_file_extension tbr.consolidate(new_resource_file) tbr.newUuid() sanitize_dataset_tags(tbr) tbr.write(output_file) return output_file
def __gather_contigset(input_files, output_file, new_resource_file): """Copied from pbcoretools.chunking.gather:__gather_contigset() """ skip_empty = True if skip_empty: _input_files = [] for file_name in input_files: cs = ContigSet(file_name) if len(cs.toExternalFiles()) > 0: _input_files.append(file_name) input_files = _input_files tbr = ContigSet(*input_files) tbr.consolidate(new_resource_file) tbr.newUuid() tbr.write(output_file, relPaths=True) return output_file