INNER CODE UNIT · Python

get_sequence_names

nickjcroucher/gubbins · python/gubbins/PreProcessFasta.py:107

    def get_sequence_names(self):
        sequence_names = []
        with open(self.input_filename) as input_handle:
            alignments = AlignIO.parse(input_handle, "fasta")
            for alignment in alignments:
                for record in alignment:
                    sequence_names.append(record.id)
        return sequence_names
    
    def get_alignment_length(self, format = "fasta"):
        alignment = AlignIO.read(self.input_filename, format)
        return alignment.get_alignment_length()

    def get_alignment_information(self, format = "fasta"):
        sequence_names = []
        base_frequencies = [0,0,0,0]
        alignment = AlignIO.read(self.input_filename, format)
        alignment_length = alignment.get_alignment_length()

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