allpy: 3bdcee61356d test/usecase3.py

allpy

view test/usecase3.py @ 668:3bdcee61356d

blocks3d/www: fix log-file caused bug of building r2w was configured to use /tmp/blocks3d-www-build.log. It caused build error if this file has been creted by other user. Log-file path was changed to ./output/blocks3d-www-build.log Makefile was changed to create ./output directory before running r2w

author	boris (kodomo) <bnagaev@gmail.com>
date	Fri, 01 Jul 2011 10:32:37 +0400
parents	fb5b4f87d741
children	ddf85d0a8924

line source

1 from allpy import protein

2 from allpy.processors import Left

3 import sys

5 ranges = [(0,5), (7,12)]

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

8 for begin, end in ranges:

9 columns = alignment.columns[begin:end]

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

11 alignment.remove_gap_columns()

12 alignment.to_file(sys.stdout)

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