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)
motif = Motif(alphabet, instances=instances)
else:
raise ValueError("Unknown format %s" % format)
motif.mask = "*" * motif.length
return motif
def read(handle):
"""read(handle)"""
record = Record()
record.ver = next(handle)
record.cmd_line = next(handle)
for line in handle:
if line.strip() == "":
pass
elif line[:4] == "Para":
record.param_dict = {}
elif line[0] == "#":
seq_name = line.split("\t")[1]
record.seq_dict.append(seq_name)
elif "=" in line:
par_name = line.split("=")[0].strip()
par_value = line.split("=")[1].strip()
record.param_dict[par_name] = par_value
elif line[:5] == "Input":
record.seq_dict = []
elif line[:5] == "Motif":
record.current_motif = Motif()
record.motifs.append(record.current_motif)
record.current_motif.alphabet = IUPAC.unambiguous_dna
elif line[:3] == "MAP":
record.current_motif.score = float(line.split()[-1])
elif len(line.split("\t")) == 4:
seq = Seq(line.split("\t")[0], IUPAC.unambiguous_dna)
record.current_motif.add_instance(seq)
elif "*" in line:
record.current_motif.set_mask(line.strip("\n\c"))
else:
raise ValueError(line)
return record
def construct_weblogo(self, weblogo_filename, weblogo_revcompl_filename):
self.weblogo_basename = os.path.basename(weblogo_filename)
self.weblogo_revcompl_basename = os.path.basename(
weblogo_revcompl_filename)
motif = Motif(alphabet=IUPAC.unambiguous_dna)
for kmer in self.kmer_lst:
motif.add_instance(Seq(kmer, motif.alphabet))
logowidth_normal = self.construct_weblogo_helper(
weblogo_filename, motif)
#reverse complement
motif_revcompl = motif.reverse_complement()
logowidth_revcompl = self.construct_weblogo_helper(
weblogo_revcompl_filename, motif_revcompl)
self.logowidth = max(self.logowidth, logowidth_normal,
logowidth_revcompl)
def read(handle):
"""read(handle)"""
record = Record()
line = handle.next()
record.version = line.strip()
line = handle.next()
record.command = line.strip()
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":
motif = Motif(IUPAC.unambiguous_dna, instances)
motif.score = float(line.split()[-1])
motif.number = number
motif.set_mask(mask)
record.motifs.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
def read(handle):
"""read(handle)"""
record = Record()
line = handle.next()
record.version = line.strip()
line = handle.next()
record.command = line.strip()
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":
current_motif = Motif()
current_motif.alphabet = IUPAC.unambiguous_dna
record.motifs.append(current_motif)
elif line[:3] == "MAP":
current_motif.score = float(line.split()[-1])
elif len(line.split("\t")) == 4:
seq = Seq(line.split("\t")[0], IUPAC.unambiguous_dna)
current_motif.add_instance(seq)
elif "*" in line:
current_motif.set_mask(line.strip("\n\c"))
else:
raise ValueError(line)
return record
def motif(self, line):
self.current_motif = Motif()
self.motifs.append(self.current_motif)
self.current_motif.alphabet = IUPAC.unambiguous_dna
