Mercurial > repos > estrain > microrunqc
annotate median_size.py @ 8:fdf81f8a707e draft
Uploaded
| author | estrain |
|---|---|
| date | Fri, 10 Mar 2023 15:43:08 +0000 |
| parents | a53acd38d77e |
| children |
| rev | line source |
|---|---|
| 0 | 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) |