INNER CODE UNIT · Python

get_chain

hillerlab/TOGA · CESAR_wrapper.py:539

def get_chain(chain_file, chain_id):
    """Return chain string according the parameters passed."""
    chain = None  # to calm IDE down
    if chain_file.endswith(".bst"):
        # we have bdb file; extract with BDB extractor
        chain = chain_extract_id(chain_file, chain_id)
        return chain
    elif chain_file.endswith(".gz"):  # a gzipped chain file was given
        # gzip and redirect scteam to chain_filter_by_id binary
        extract_by_id_cmd = (
            f"gzip -dc {chain_file} | ./modules/chain_filter_by_id stdin {chain_id}"
        )
        try:  # check that output is OK
            chain = subprocess.check_output(extract_by_id_cmd, shell=True).decode(
                "utf-8"
            )
        except subprocess.CalledProcessError:
            # die if the command died

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