INNER CODE UNIT · Python

parse

pha4ge/hAMRonization · hAMRonization/AmrFinderPlusIO.py:72

    def parse(self, handle):
        """
        Read each and return it
        """
        skipped_truncated = 0
        reader = csv.DictReader(handle, delimiter="\t")
        for result in reader:

            # Replace NA value with None for consistency
            for field, value in result.items():
                if value == "NA":
                    result[field] = None

            # Skip reported virulence genes
            if result['Type'] == "VIRULENCE":
                continue

            # AFP reports partial hits so to avoid misleadingly listing these

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