INNER CODE UNIT · Python

parse

pha4ge/hAMRonization · hAMRonization/__init__.py:85

def parse(handle, metadata, tool):
    r"""Turn a sequence file into an iterator returning SeqRecords.
    Arguments:
     - handle   - handle to the file, or the filename as a string
     - tool - lower case string describing the file format.
     - required_arguments - dict containing the required arguments for tool
    Typical usage, opening a file to read in, and looping over the record(s):
    >>> import hAMRonization as hAMR
    >>> filename = "abricate_report.tsv"
    >>> metadata = {"analysis_software_version": "1.0.1",
    ...             "reference_database_version": "2019-Jul-28"}
    >>> for result in hAMR.parse(filename, required_arguments, "abricate"):
    ...    print(result)

    """
    if not isinstance(tool, str):
        raise TypeError("Need a string for the file format (lower case)")
    if not isinstance(metadata, dict):

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