Mercurial > repos > estrain > microrunqc
view median_size.py @ 0:4e629e82c5b1 draft default tip
planemo upload commit a820b38dea9a409c11e220ba904da232fdbc4c05
| author | estrain |
|---|---|
| date | Fri, 13 Mar 2026 12:51:10 +0000 |
| parents | |
| children |
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#!/usr/bin/env ## Errol Strain (estrain@gmail.com) ## calculate median insert size from sam file import numpy as np def get_data(infile): lengths = [] for line in infile: if line.startswith('@'): pass else: line = line.rsplit() length = int(line[8]) if length > 0: lengths.append(length) else: pass return lengths if __name__ == "__main__": import sys lengths = get_data(sys.stdin) md = int(np.median(lengths)) print(md)
