Exemplo n.º 1
0
def _mkneg(fname,window,ftr,pssm = False):
	with open(fname) as fp:
		neg = [i[0] for i in mkftr.getseq(fp)]
		# ? didn't idchoice() need ? 
		for cnt,group in enumerate(mkftr.idchoice(neg)):
			fp.seek(0)
			for negid,seq in mkftr.getseq(fp):
				if pssm:
					# For PSSM
					seq = [int(i) for i in seq.split()]
					if len(seq) < 100:
						continue
				else:
					if len(seq) < 100 or seq.find('X') > 0:
						continue
				if negid in group:
					_indx = [i for i in range(1,len(seq))]
					random.shuffle(_indx)
					yield negid,{pos:(-1,mkvec(ftr,seq,window,pos,pssm = pssm)) for pos in sorted(_indx[:5])}
Exemplo n.º 2
0
def _mkdtst(window,ftr,represent = 'dataset/sugar.txt',
			answer = 'dataset/answer_sugar.txt',
			name = 'sugar',
			flg = True,pssm = False):
	
	def ans2int(ans,idch,pos):
		if ans.isans(idch,pos):
			return 1
		return -1

	with open(represent) as fp:
		lid = [line.strip() for line in iter(fp.readline,'')]
	ans_sgr = mkftr.ans(answer)
	# ? Dose idchoice need ?
	for cnt,group in enumerate(mkftr.idchoice(lid)):
		for idch,start,seq in mkftr.slider(group,name,pssm = pssm):
			idch = idch.strip()
			# 2012/1/31 pos -> pos + start
			# !!! now nodyfying !!!
			yield idch,{pos:(ans2int(ans_sgr,idch,start + pos),mkvec(ftr,seq,window,pos,pssm = pssm))
						for pos in range(len(seq)) if ans_sgr.isans(idch,start + pos) or not flg}
			# !!! now modfying !!!
			
			"""