INNER CODE UNIT · Python

read_fasta

cbg-ethz/V-pipe · workflow/scripts/alignmentIntervals.py:79

def read_fasta(fasta_file):
    "Parse fasta file"
    count = 0
    headers = []
    sequences = []
    aux = []
    with open(fasta_file, "r") as infile:
        for line in infile:
            record = line.rstrip()
            if record and record[0] == ">":
                headers.append(record[1:])
                if count > 0:
                    sequences.append("".join(aux))
                    aux = []
            else:
                aux.append(record)
            count += 1

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