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
