Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.fbb.msu.ru/hg/allpy/annotate/73f9779491ef/test/test.py
Дата изменения: Unknown
Дата индексирования: Sun Mar 2 02:35:41 2014
Кодировка:
allpy: test/test.py annotate

allpy

annotate test/test.py @ 191:73f9779491ef

Renamed lib to allpy Previously, every import looked like "from allpy.lib import ...", which was ridiculous. Consequences: 1. Uses of the package look like "from allpy import" 2. When testing the package locally, you have to add `pwd` to PYTHONPATH, not `pwd`/.. (this is a good thing (tm)) 3. It is now possible to make a proper Debian package The change renames directory & fixes all imports referencing allpy.lib The results are untested since there were no working tests before the change.
author Daniil Alexeyevsky <me.dendik@gmail.com>
date Thu, 18 Nov 2010 19:38:05 +0300
parents fb3164f03984
children faa7e19bffd9
rev   line source
bnagaev@98 1 import sys
bnagaev@83 2
me@191 3 from allpy.alignment import Alignment
me@191 4 from allpy.block import Block
bnagaev@83 5
bnagaev@175 6 p = Alignment(open('test.fasta'))
bnagaev@83 7 print "alignment length: %i" % len(p)
bnagaev@110 8 print "sequence: %s" % str(p.sequences[0])
bnagaev@83 9
bnagaev@120 10 p.sequences[0].pdb_chain_add(open('1jcc.pdb'), '1jcc', 'B')
bnagaev@120 11 p.sequences[1].pdb_chain_add(open('1kfm.pdb'), '1kfm', 'A')
bnagaev@120 12
bnagaev@121 13 b = Block(p)
bnagaev@130 14 GCs = b.geometrical_cores(ac_new_atoms=0.00, ac_count=-1)
bnagaev@128 15 b.save_fasta(sys.stdout)
bnagaev@134 16 for i, GC in enumerate(GCs):
bnagaev@134 17 GC.save_xstring(sys.stdout, i)
bnagaev@121 18
bnagaev@110 19 #~ p.muscle_align()
bnagaev@110 20 #~ p.save_fasta(sys.stdout)