INNER CODE UNIT · Python

__init__

nickjcroucher/gubbins · python/gubbins/PreProcessFasta.py:13

    def __init__(self, input_filename, verbose=False, filter_percentage=25):
        self.input_filename = input_filename
        self.verbose = verbose
        self.filter_percentage = filter_percentage

    def hash_sequences(self):
        sequence_hash_to_taxa = defaultdict(list)
        with open(self.input_filename) as input_handle:
            alignments = AlignIO.parse(input_handle, "fasta")
            for alignment in alignments:
                for record in alignment:
                    sequence_hash = hashlib.md5()
                    sequence_hash.update(str(record.seq).encode('utf-8'))
                    hash_of_sequence = sequence_hash.digest()
                    sequence_hash_to_taxa[hash_of_sequence].append(record.id)

                    if self.verbose:
                        print("Sample " + str(record.id) + " has a hash of " + str(hash_of_sequence))

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