Mercurial > repos > estrain > microrunqc
diff median_size.py @ 2:25a92dfb780a draft
Uploaded
author | estrain |
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date | Fri, 10 Mar 2023 13:22:58 +0000 |
parents | a53acd38d77e |
children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/median_size.py Fri Mar 10 13:22:58 2023 +0000 @@ -0,0 +1,26 @@ +#!/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)