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pscoils

Timestamp:

06/10/08 23:46:02 (4 years ago)

Author:

mauro

Message:

Files:

r24	r27
2	2	import sys
3	3	import biocomp.pscoils
	4	from biocomp.pscoils import pred_coil
	5	from biocomp.pscoils.utils import readFasta, printCoil
4	6	import getopt
5	7	import string
	8	from Bio.SeqRecord import SeqRecord
6	9
7	10	def usage(prog):
…	…
31	34	for o,a in opts:
32	35	if o == '-f':
33		seqs=~~biocomp.pscoils.~~readFasta(a)
	36	seqs=readFasta(a)
34	37	modefasta=True
35	38	elif o == '-p':
…	…
55	58	#use both
56	59	for name in seqs.keys(): # WARNING We assume only one sequence!!!
57		gg,gcc,prob,hept_seq,score=biocomp.pscoils.pred_coil2(seqs[name],prof,params,wlambda)
58		biocomp.pscoils.printCoil(seqs[name],len(seqs[name]),hept_seq,score,prob,gcc,gg,labels)
	60	# TODO
	61	raise("TODO")
	62	gg,gcc,prob,hept_seq,score=biocomp.pscoils.pred_coil2(seqs[name],prof,params,wlambda)
	63	printCoil(seqs[name],len(seqs[name]),hept_seq,score,prob,gcc,gg,labels)
59	64	elif modefasta:
60	65	for name in seqs.keys():
61		gg,gcc,prob,hept_seq,score=biocomp.pscoils.pred_coil(seqs[name],len(seqs[name]),params,biocomp.pscoils.seqScore)
62		biocomp.pscoils.printCoil(seqs[name],len(seqs[name]),hept_seq,score,prob,gcc,gg,labels)
	66	seqr = SeqRecord(seqs[name], id=name)
	67	seqr = pred_coil(seqr, params)
	68	printCoil(seqr,labels)
63	69	elif modeprofile:
	70	# TODO
	71	raise("TODO")
64	72	gg,gcc,prob,hept_seq,score=biocomp.pscoils.pred_coil(prof,profLen,params,biocomp.pscoils.profScore)
65	73	biocomp.pscoils.printCoil('x'*profLen,profLen,hept_seq,score,prob,gcc,gg,labels)