Mercurial > repos > estrain > microrunqc

comparison median_size.py @ 0:a53acd38d77e draft

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author estrain
date Tue, 24 Mar 2020 08:54:42 -0400
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-1:000000000000 0:a53acd38d77e
1 #!/usr/bin/env
2
3 ## Errol Strain (estrain@gmail.com)
4 ## calculate median insert size from sam file
5
6 import numpy as np
7
8 def get_data(infile):
9 lengths = []
10 for line in infile:
11 if line.startswith('@'):
12 pass
13 else:
14 line = line.rsplit()
15 length = int(line[8])
16 if length > 0:
17 lengths.append(length)
18 else:
19 pass
20 return lengths
21
22 if __name__ == "__main__":
23 import sys
24 lengths = get_data(sys.stdin)
25 md = int(np.median(lengths))
26 print(md)