INNER CODE UNIT · Python

SPECIES_LEVEL_AVERAGE_IDENTITY

wwood/singlem · singlem/main.py:35

SPECIES_LEVEL_AVERAGE_IDENTITY = float(DEFAULT_WINDOW_SIZE - SearchPipe.DEFAULT_MAX_SPECIES_DIVERGENCE) / DEFAULT_WINDOW_SIZE


def seqs(args):
    from singlem.sequence_classes import SeqReader as SingleMSeqReader
    from singlem.metagenome_otu_finder import MetagenomeOtuFinder

    if args.alignment_type == 'aa':
        is_protein_alignment = True
    elif args.alignment_type == 'dna':
        is_protein_alignment = False
    else:
        raise Exception("Unexpected alignment type '%s'" % args.alignment_type)

    # Read in the fasta Alignment
    protein_alignment = SingleMSeqReader().alignment_from_alignment_file(args.alignment)
    logging.info("Read in %i aligned protein sequences e.g. %s %s" % (
        len(protein_alignment),

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