File: maf_gc_content.py

package info (click to toggle)
python-bx 0.13.0-1
  • links: PTS, VCS
  • area: main
  • in suites: forky, sid, trixie
  • size: 5,000 kB
  • sloc: python: 17,136; ansic: 2,326; makefile: 24; sh: 8
file content (31 lines) | stat: -rwxr-xr-x 585 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
#!/usr/bin/python3

"""
Read a MAF from standard input and print average GC content of each alignment

usage: %prog < maf > out
"""

import sys

from bx.align import maf


def __main__():
    maf_reader = maf.Reader(sys.stdin)

    for m in maf_reader:
        gc = 0
        bases = 0
        for c in m.components:
            gc += c.text.count("G")
            gc += c.text.count("C")
            gc += c.text.count("g")
            gc += c.text.count("c")
            bases += len(c.text) - c.text.count("-")

        print(gc / bases)


if __name__ == "__main__":
    __main__()