allpy: test/test.py annotate

allpy

add fileio module, remove fasta module, add msf support (see #31)

author	boris (netbook) <bnagaev@gmail.com>
date	Fri, 11 Feb 2011 15:04:17 +0300
parents	73f9779491ef
children

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
dendik@406	19 #~ alignment.process(processors.Muscle())
bnagaev@110	20 #~ p.save_fasta(sys.stdout)