def read(handle, format):
alphabet = IUPAC.unambiguous_dna
counts = {}
if format == "pfm":
# reads the motif from Jaspar .pfm file
letters = "ACGT"
for letter, line in zip(letters, handle):
words = line.split()
#if there is a letter in the beginning, ignore it
if words[0] == letter:
words = words[1:]
counts[letter] = map(float, words)
motif = Motif(alphabet, counts=counts)
elif format == "sites":
# reads the motif from Jaspar .sites file
instances = []
for line in handle:
if not line.startswith(">"):
break
# line contains the header ">...."
# now read the actual sequence
line = handle.next()
instance = ""
for c in line.strip():
if c == c.upper():
instance += c
instance = Seq(instance, alphabet)
instances.append(instance)
instances = Instances(instances, alphabet)
motif = Motif(alphabet, instances=instances)
else:
raise ValueError("Unknown format %s" % format)
motif.mask = "*" * motif.length
return motif
def read(handle):
"""Parse an AlignACE format handle as a Record object."""
record = Record()
line = next(handle)
record.version = line.strip()
line = next(handle)
record.command = line.strip()
mask = None
number = None
for line in handle:
line = line.strip()
if line == "":
pass
elif line[:4] == "Para":
record.parameters = {}
elif line[0] == "#":
seq_name = line.split("\t")[1]
record.sequences.append(seq_name)
elif "=" in line:
par_name, par_value = line.split("=")
par_name = par_name.strip()
par_value = par_value.strip()
record.parameters[par_name] = par_value
elif line[:5] == "Input":
record.sequences = []
elif line[:5] == "Motif":
words = line.split()
assert words[0] == "Motif"
number = int(words[1])
instances = []
elif line[:3] == "MAP":
alphabet = "ACGT"
instances = Instances(instances, alphabet)
motif = Motif(alphabet, instances)
motif.score = float(line.split()[-1])
motif.number = number
motif.mask = mask
record.append(motif)
elif len(line.split("\t")) == 4:
seq = Seq(line.split("\t")[0])
instances.append(seq)
elif "*" in line:
mask = line.strip("\r\n")
else:
raise ValueError(line)
return record
def read(handle):
"""read(handle)"""
record = Record()
line = next(handle)
record.version = line.strip()
line = next(handle)
record.command = line.strip()
mask = None
number = None
for line in handle:
line = line.strip()
if line == "":
pass
elif line[:4] == "Para":
record.parameters = {}
elif line[0] == "#":
seq_name = line.split("\t")[1]
record.sequences.append(seq_name)
elif "=" in line:
par_name, par_value = line.split("=")
par_name = par_name.strip()
par_value = par_value.strip()
record.parameters[par_name] = par_value
elif line[:5] == "Input":
record.sequences = []
elif line[:5] == "Motif":
words = line.split()
assert words[0] == "Motif"
number = int(words[1])
instances = []
elif line[:3] == "MAP":
alphabet = IUPAC.unambiguous_dna
instances = Instances(instances, alphabet)
motif = Motif(alphabet, instances)
motif.score = float(line.split()[-1])
motif.number = number
motif.mask = mask
record.append(motif)
elif len(line.split("\t")) == 4:
seq = Seq(line.split("\t")[0], IUPAC.unambiguous_dna)
instances.append(seq)
elif "*" in line:
mask = line.strip("\r\n")
else:
raise ValueError(line)
return record