def parse(self, fo):
motifs = []
p = re.compile(
r'^\d+\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)')
pwm = []
motif_id = ""
for line in fo.readlines():
if line.startswith("Motif #"):
if pwm:
m = Motif(pwm)
m.id = "BioProspector_w%s_%s" % (len(m), motif_id)
motifs.append(m)
motif_id = line.split("#")[1].split(":")[0]
pwm = []
else:
m = p.search(line)
if m:
pwm.append(
[float(m.group(x)) / 100.0 for x in range(1, 5)])
if pwm:
m = Motif(pwm)
m.id = "BioProspector_w%s_%s" % (len(m), motif_id)
motifs.append(m)
return motifs
def parse(self, fo):
"""
Convert BioProspector output to motifs
Parameters
----------
fo : file-like
File object containing BioProspector output.
Returns
-------
motifs : list
List of Motif instances.
"""
motifs = []
p = re.compile(
r"^\d+\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)")
pwm = []
motif_id = ""
for line in fo.readlines():
if line.startswith("Motif #"):
if pwm:
m = Motif(pwm)
m.id = "BioProspector_w%s_%s" % (len(m), motif_id)
motifs.append(m)
motif_id = line.split("#")[1].split(":")[0]
pwm = []
else:
m = p.search(line)
if m:
pwm.append(
[float(m.group(x)) / 100.0 for x in range(1, 5)])
if pwm:
m = Motif(pwm)
m.id = "BioProspector_w%s_%s" % (len(m), motif_id)
motifs.append(m)
return motifs
def parse(self, fo):
motifs = []
p = re.compile(r'^\d+\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)')
pwm = []
motif_id = ""
for line in fo.readlines():
if line.startswith("Motif #"):
if pwm:
m = Motif(pwm)
m.id = "BioProspector_w%s_%s" % (len(m), motif_id)
motifs.append(m)
motif_id = line.split("#")[1].split(":")[0]
pwm = []
else:
m = p.search(line)
if m:
pwm.append([float(m.group(x))/100.0 for x in range(1,5)])
if pwm:
m = Motif(pwm)
m.id = "BioProspector_w%s_%s" % (len(m), motif_id)
motifs.append(m)
return motifs
