def _parse(self):
i = 0
while i < len(self.lines):
line = self.lines[i]
toks = line.split()
if '-i' in toks and not self.fastafile:
idx = toks.index('-i')
self.fastafile = toks[idx+1]
if (len(toks) > 0 and toks[0] == 'Motif'):
seqs = []
while 1:
i = i + 1
line = self.lines[i]
toks = line.split()
if toks[0][0] == '*': break
seqs.append(toks[0])
M = Motif(seqs)
i = i + 1
line = self.lines[i]
toks = line.split()
MAP = float(toks[2])
if MAP > 1000: MAP = 0 #likely to be an AlignACE error
M.MAP = MAP
self.motifs.append(M)
i = i + 1
self.nmotifs = len(self.motifs)
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)
