Created
March 7, 2023 09:42
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Quality trimming experiment
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| #!/usr/bin/env python3 | |
| """Quality trimming using a running sum from the 5' to 3' end""" | |
| import sys | |
| from argparse import ArgumentParser | |
| import dnaio | |
| def qual_trim_index(qualities_ascii, threshold): | |
| qualities = [ord(c) - 33 for c in qualities_ascii] | |
| score = 0 | |
| best_end = 0 | |
| best_score = 0 | |
| for i, q in enumerate(qualities): | |
| score += q - threshold | |
| if score > best_score: | |
| best_end = i + 1 | |
| best_score = score | |
| return best_end | |
| def main(): | |
| parser = ArgumentParser() | |
| parser.add_argument("-q", dest="threshold", metavar="THRESHOLD", type=int, default=30, help="Quality trimming threshold") | |
| parser.add_argument("fastq") | |
| args = parser.parse_args() | |
| threshold = args.threshold | |
| with dnaio.open(args.fastq) as infile: | |
| with dnaio.open(sys.stdout.buffer, mode="w", qualities=True) as outfile: | |
| for record in infile: | |
| end = qual_trim_index(record.qualities, threshold) | |
| record = record[:end] | |
| outfile.write(record) | |
| if __name__ == "__main__": | |
| main() |
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