INNER CODE UNIT · Python

fasta_parse

torognes/swarm · scripts/amplicon_contingency_table.py:23

def fasta_parse():
    """
    Map amplicon ids, abundances and samples
    """
    separator = ";size="
    fasta_files = sys.argv[1:]
    all_amplicons = dict()
    samples = dict()
    amplicons2samples = dict()
    for fasta_file in fasta_files:
        sample = os.path.basename(fasta_file)
        sample = os.path.splitext(sample)[0]
        samples[sample] = samples.get(sample, 0) + 1
        with open(fasta_file, "r") as fasta_file:
            for line in fasta_file:
                if line.startswith(">"):
                    amplicon, abundance = line.strip(">;\n").split(separator)
                    abundance = int(abundance)

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