def _parse(self): 'Parse MDscan file' alloutput = '\n'.join(self.lines) premotifs = alloutput.split('\nMtf ') print len(premotifs) for pm in premotifs: sublines = pm.split('\n') score, seednum = 0, 0 seqs = [] for line in sublines: if line.find('Final Motif') == 0: toks = line.split() score = float(toks[6]) seednum = int(toks[8]) if line.find('>') == 0: seqs.append(line.split()[-1]) #print "SEQS: ",seqs if seqs: m = Motif(seqs) m.MAP = score m.seednum = seednum self.motifs.append(m)
def _parse(self): 'Parse MDscan file' alloutput = '\n'.join(self.lines) premotifs = alloutput.split('\nMtf ') print len(premotifs) for pm in premotifs: sublines = pm.split('\n') score, seednum = 0,0 seqs = [] for line in sublines: if line.find('Final Motif') == 0: toks = line.split() score = float(toks[6]) seednum = int(toks[8]) if line.find('>') == 0: seqs.append(line.split()[-1]) #print "SEQS: ",seqs if seqs: m = Motif(seqs) m.MAP = score m.seednum = seednum self.motifs.append(m)