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.set_mask("*"*motif.length)
return motif
class AlignAceConsumer:
"""
The general purpose consumer for the AlignAceScanner (DEPRECATED).
Should be passed as the consumer to the feed method of the AlignAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property.
This class is DEPRECATED; please use the read() function in this module
instead.
"""
def __init__(self):
import warnings
warnings.warn(
"Bio.Motif.Parsers.AlignAce.AlignAceConsumer is deprecated; please use the read() function in this module instead.",
Bio.BiopythonDeprecationWarning)
self.motifs = []
self.current_motif = None
self.param_dict = None
def parameters(self, line):
self.param_dict = {}
def parameter(self, line):
par_name = line.split("=")[0].strip()
par_value = line.split("=")[1].strip()
self.param_dict[par_name] = par_value
def sequences(self, line):
self.seq_dict = []
def sequence(self, line):
seq_name = line.split("\t")[1]
self.seq_dict.append(seq_name)
def motif(self, line):
self.current_motif = Motif()
self.motifs.append(self.current_motif)
self.current_motif.alphabet = IUPAC.unambiguous_dna
def motif_hit(self, line):
seq = Seq(line.split("\t")[0], IUPAC.unambiguous_dna)
self.current_motif.add_instance(seq)
def motif_score(self, line):
self.current_motif.score = float(line.split()[-1])
def motif_mask(self, line):
self.current_motif.set_mask(line.strip("\n\c"))
def noevent(self, line):
pass
def version(self, line):
self.ver = line
def command_line(self, line):
self.cmd_line = line
class AlignAceConsumer(object):
"""
The general purpose consumer for the AlignAceScanner (DEPRECATED).
Should be passed as the consumer to the feed method of the AlignAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property.
This class is DEPRECATED; please use the read() function in this module
instead.
"""
def __init__(self):
import warnings
warnings.warn("Bio.Motif.Parsers.AlignAce.AlignAceConsumer is deprecated; please use the read() function in this module instead.", Bio.BiopythonDeprecationWarning)
self.motifs=[]
self.current_motif=None
self.param_dict = None
def parameters(self,line):
self.param_dict={}
def parameter(self,line):
par_name = line.split("=")[0].strip()
par_value = line.split("=")[1].strip()
self.param_dict[par_name]=par_value
def sequences(self,line):
self.seq_dict=[]
def sequence(self,line):
seq_name = line.split("\t")[1]
self.seq_dict.append(seq_name)
def motif(self,line):
self.current_motif = Motif()
self.motifs.append(self.current_motif)
self.current_motif.alphabet=IUPAC.unambiguous_dna
def motif_hit(self,line):
seq = Seq(line.split("\t")[0],IUPAC.unambiguous_dna)
self.current_motif.add_instance(seq)
def motif_score(self,line):
self.current_motif.score = float(line.split()[-1])
def motif_mask(self,line):
self.current_motif.set_mask(line.strip("\n\c"))
def noevent(self,line):
pass
def version(self,line):
self.ver = line
def command_line(self,line):
self.cmd_line = line
class AlignAceConsumer:
"""
The general purpose consumer for the AlignAceScanner.
Should be passed as the consumer to the feed method of the AlignAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property.
"""
def __init__(self):
self.motifs = []
self.current_motif = None
self.param_dict = None
def parameters(self, line):
self.param_dict = {}
def parameter(self, line):
par_name = line.split("=")[0].strip()
par_value = line.split("=")[1].strip()
self.param_dict[par_name] = par_value
def sequences(self, line):
self.seq_dict = []
def sequence(self, line):
seq_name = line.split("\t")[1]
self.seq_dict.append(seq_name)
def motif(self, line):
self.current_motif = Motif()
self.motifs.append(self.current_motif)
self.current_motif.alphabet = IUPAC.unambiguous_dna
def motif_hit(self, line):
seq = Seq(line.split("\t")[0], IUPAC.unambiguous_dna)
self.current_motif.add_instance(seq)
def motif_score(self, line):
self.current_motif.score = float(line.split()[-1])
def motif_mask(self, line):
self.current_motif.set_mask(line.strip("\n\c"))
def noevent(self, line):
pass
def version(self, line):
self.ver = line
def command_line(self, line):
self.cmd_line = line
class AlignAceConsumer:
"""
The general purpose consumer for the AlignAceScanner.
Should be passed as the consumer to the feed method of the AlignAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property.
"""
def __init__(self):
self.motifs = []
self.current_motif = None
self.param_dict = None
def parameters(self, line):
self.param_dict = {}
def parameter(self, line):
par_name = line.split("=")[0].strip()
par_value = line.split("=")[1].strip()
self.param_dict[par_name] = par_value
def sequences(self, line):
self.seq_dict = []
def sequence(self, line):
seq_name = line.split("\t")[1]
self.seq_dict.append(seq_name)
def motif(self, line):
self.current_motif = Motif()
self.motifs.append(self.current_motif)
self.current_motif.alphabet = IUPAC.unambiguous_dna
def motif_hit(self, line):
seq = Seq(line.split("\t")[0], IUPAC.unambiguous_dna)
self.current_motif.add_instance(seq)
def motif_score(self, line):
self.current_motif.score = float(line.split()[-1])
def motif_mask(self, line):
self.current_motif.set_mask(line.strip("\n\c"))
def noevent(self, line):
pass
def version(self, line):
self.ver = line
def command_line(self, line):
self.cmd_line = line
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":
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 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
