allpy: 06dbba0b65a3 test/usecase3.py

allpy

pair-cores/wt: add g++ 4.5 to deps

author	Boris Nagaev <bnagaev@gmail.com>
date	Fri, 09 Mar 2012 00:20:43 +0400
parents	e7d60bf1dfd8
children	08d892230e8c

line source

1 #!/usr/bin/python

2 from allpy import protein

3 from allpy.processors import Left

4 from allpy.util import open

5 import sys

7 if __name__ == "__main__":

8 ranges = sys.argv[1]

9 infile = open(sys.argv[2])

10 outfile = open(sys.argv[3])

12 # This accepts ranges in form "0:5,7:12,1:-1"

13 ranges = [map(int, range.split(':')) for range in ranges.split(',')]

15 alignment = protein.Alignment().append_file(sys.stdin)

16 for begin, end in ranges:

17 columns = alignment.columns[begin:end]

18 protein.Block.from_alignment(alignment, columns=columns).realign(Left())

19 alignment.remove_gap_columns()

20 alignment.to_file(sys.stdout)

22 # vim: set et ts=4 sts=4 sw=4: