parse_input_files.py 文件源码

def convert(pheno):
    # suppress Exceptions so that we can report back on which phenotypes succeeded and which didn't.
    try:
        with VariantFileWriter(common_filepaths['parsed'](pheno['phenocode'])) as writer:
            pheno_reader = PhenoReader(pheno, minimum_maf=conf.assoc_min_maf)
            variants = pheno_reader.get_variants()
            if conf.quick: variants = itertools.islice(variants, 0, 10000)
            writer.write_all(variants)
    except Exception as exc:
        import traceback
        yield {
            'type': 'warning', # TODO: make PerPhenoParallelizer print this.
            'warning_str':
                'Exception:\n' + indent(str(exc)) +
                '\nTraceback:\n' + indent(traceback.format_exc()) +
                '\nFiles:\n' + indent('\n'.join(pheno['assoc_files']))
        }
        yield {"succeeded": False, "exception_str": str(exc), "exception_tb": traceback.format_exc()}
    else:
        yield {"succeeded": True}