def __next__(self):
handle = self.handle
try:
# Header we saved from when we were parsing
# the previous alignment.
line = self._header
del self._header
except AttributeError:
line = handle.readline()
if not line:
raise StopIteration
# Whitelisted headers we know about
known_headers = ['CLUSTAL', 'PROBCONS', 'MUSCLE', 'MSAPROBS']
if line.strip().split()[0] not in known_headers:
raise ValueError(
"%s is not a known CLUSTAL header: %s" %
(line.strip().split()[0], ", ".join(known_headers)))
# find the clustal version in the header line
version = None
for word in line.split():
if word[0] == '(' and word[-1] == ')':
word = word[1:-1]
if word[0] in '0123456789':
version = word
break
# There should be two blank lines after the header line
line = handle.readline()
while line.strip() == "":
line = handle.readline()
# If the alignment contains entries with the same sequence
# identifier (not a good idea - but seems possible), then this
# dictionary based parser will merge their sequences. Fix this?
ids = []
seqs = []
consensus = ""
seq_cols = None # Used to extract the consensus
# Use the first block to get the sequence identifiers
while True:
if line[0] != " " and line.strip() != "":
# Sequences identifier...
fields = line.rstrip().split()
# We expect there to be two fields, there can be an optional
# "sequence number" field containing the letter count.
if len(fields) < 2 or len(fields) > 3:
raise ValueError("Could not parse line:\n%s" % line)
ids.append(fields[0])
seqs.append(fields[1])
# Record the sequence position to get the consensus
if seq_cols is None:
start = len(fields[0]) + line[len(fields[0]):].find(
fields[1])
end = start + len(fields[1])
seq_cols = slice(start, end)
del start, end
assert fields[1] == line[seq_cols]
if len(fields) == 3:
# This MAY be an old style file with a letter count...
try:
letters = int(fields[2])
except ValueError:
raise ValueError(
"Could not parse line, bad sequence number:\n%s" %
line)
if len(fields[1].replace("-", "")) != letters:
raise ValueError(
"Could not parse line, invalid sequence number:\n%s"
% line)
elif line[0] == " ":
# Sequence consensus line...
assert len(ids) == len(seqs)
assert len(ids) > 0
assert seq_cols is not None
consensus = line[seq_cols]
assert not line[:seq_cols.start].strip()
assert not line[seq_cols.stop:].strip()
# Check for blank line (or end of file)
line = handle.readline()
assert line.strip() == ""
break
else:
# No consensus
break
line = handle.readline()
if not line:
break # end of file
assert line.strip() == ""
assert seq_cols is not None
# Confirm all same length
for s in seqs:
assert len(s) == len(seqs[0])
if consensus:
assert len(consensus) == len(seqs[0])
# Loop over any remaining blocks...
done = False
while not done:
# There should be a blank line between each block.
# Also want to ignore any consensus line from the
# previous block.
while (not line) or line.strip() == "":
line = handle.readline()
if not line:
break # end of file
if not line:
break # end of file
if line.split(None, 1)[0] in known_headers:
# Found concatenated alignment.
done = True
self._header = line
break
for i in range(len(ids)):
assert line[0] != " ", "Unexpected line:\n%s" % repr(line)
fields = line.rstrip().split()
# We expect there to be two fields, there can be an optional
# "sequence number" field containing the letter count.
if len(fields) < 2 or len(fields) > 3:
raise ValueError("Could not parse line:\n%s" % repr(line))
if fields[0] != ids[i]:
raise ValueError(
"Identifiers out of order? Got '%s' but expected '%s'"
% (fields[0], ids[i]))
if fields[1] != line[seq_cols]:
start = len(fields[0]) + line[len(fields[0]):].find(
fields[1])
assert start == seq_cols.start, 'Old location %s -> %i:XX' % (
seq_cols, start)
end = start + len(fields[1])
seq_cols = slice(start, end)
del start, end
# Append the sequence
seqs[i] += fields[1]
assert len(seqs[i]) == len(seqs[0])
if len(fields) == 3:
# This MAY be an old style file with a letter count...
try:
letters = int(fields[2])
except ValueError:
raise ValueError(
"Could not parse line, bad sequence number:\n%s" %
line)
if len(seqs[i].replace("-", "")) != letters:
raise ValueError(
"Could not parse line, invalid sequence number:\n%s"
% line)
# Read in the next line
line = handle.readline()
# There should now be a consensus line
if consensus:
assert line[0] == " "
assert seq_cols is not None
consensus += line[seq_cols]
assert len(consensus) == len(seqs[0])
assert not line[:seq_cols.start].strip()
assert not line[seq_cols.stop:].strip()
# Read in the next line
line = handle.readline()
assert len(ids) == len(seqs)
if len(seqs) == 0 or len(seqs[0]) == 0:
raise StopIteration
if self.records_per_alignment is not None \
and self.records_per_alignment != len(ids):
raise ValueError(
"Found %i records in this alignment, told to expect %i" %
(len(ids), self.records_per_alignment))
records = (SeqRecord(Seq(s, self.alphabet), id=i, description=i)
for (i, s) in zip(ids, seqs))
alignment = MultipleSeqAlignment(records, self.alphabet)
# TODO - Handle alignment annotation better, for now
# mimic the old parser in Bio.Clustalw
if version:
alignment._version = version
if consensus:
alignment_length = len(seqs[0])
assert len(consensus) == alignment_length, \
"Alignment length is %i, consensus length is %i, '%s'" \
% (alignment_length, len(consensus), consensus)
alignment._star_info = consensus
return alignment
def next(self):
handle = self.handle
try:
#Header we saved from when we were parsing
#the previous alignment.
line = self._header
del self._header
except AttributeError:
line = handle.readline()
if not line:
raise StopIteration
#Whitelisted headers we know about
known_headers = ['CLUSTAL', 'PROBCONS', 'MUSCLE', 'MSAPROBS']
if line.strip().split()[0] not in known_headers:
raise ValueError("%s is not a known CLUSTAL header: %s" %
(line.strip().split()[0],
", ".join(known_headers)))
# find the clustal version in the header line
version = None
for word in line.split():
if word[0] == '(' and word[-1] == ')':
word = word[1:-1]
if word[0] in '0123456789':
version = word
break
#There should be two blank lines after the header line
line = handle.readline()
while line.strip() == "":
line = handle.readline()
#If the alignment contains entries with the same sequence
#identifier (not a good idea - but seems possible), then this
#dictionary based parser will merge their sequences. Fix this?
ids = []
seqs = []
consensus = ""
seq_cols = None # Used to extract the consensus
#Use the first block to get the sequence identifiers
while True:
if line[0] != " " and line.strip() != "":
#Sequences identifier...
fields = line.rstrip().split()
#We expect there to be two fields, there can be an optional
#"sequence number" field containing the letter count.
if len(fields) < 2 or len(fields) > 3:
raise ValueError("Could not parse line:\n%s" % line)
ids.append(fields[0])
seqs.append(fields[1])
#Record the sequence position to get the consensus
if seq_cols is None:
start = len(fields[0]) + line[len(fields[0]):].find(fields[1])
end = start + len(fields[1])
seq_cols = slice(start, end)
del start, end
assert fields[1] == line[seq_cols]
if len(fields) == 3:
#This MAY be an old style file with a letter count...
try:
letters = int(fields[2])
except ValueError:
raise ValueError("Could not parse line, bad sequence number:\n%s" % line)
if len(fields[1].replace("-", "")) != letters:
raise ValueError("Could not parse line, invalid sequence number:\n%s" % line)
elif line[0] == " ":
#Sequence consensus line...
assert len(ids) == len(seqs)
assert len(ids) > 0
assert seq_cols is not None
consensus = line[seq_cols]
assert not line[:seq_cols.start].strip()
assert not line[seq_cols.stop:].strip()
#Check for blank line (or end of file)
line = handle.readline()
assert line.strip() == ""
break
else:
#No consensus
break
line = handle.readline()
if not line:
break # end of file
assert line.strip() == ""
assert seq_cols is not None
#Confirm all same length
for s in seqs:
assert len(s) == len(seqs[0])
if consensus:
assert len(consensus) == len(seqs[0])
#Loop over any remaining blocks...
done = False
while not done:
#There should be a blank line between each block.
#Also want to ignore any consensus line from the
#previous block.
while (not line) or line.strip() == "":
line = handle.readline()
if not line:
break # end of file
if not line:
break # end of file
if line.split(None, 1)[0] in known_headers:
#Found concatenated alignment.
done = True
self._header = line
break
for i in range(len(ids)):
assert line[0] != " ", "Unexpected line:\n%s" % repr(line)
fields = line.rstrip().split()
#We expect there to be two fields, there can be an optional
#"sequence number" field containing the letter count.
if len(fields) < 2 or len(fields) > 3:
raise ValueError("Could not parse line:\n%s" % repr(line))
if fields[0] != ids[i]:
raise ValueError("Identifiers out of order? Got '%s' but expected '%s'"
% (fields[0], ids[i]))
if fields[1] != line[seq_cols]:
start = len(fields[0]) + line[len(fields[0]):].find(fields[1])
assert start == seq_cols.start, 'Old location %s -> %i:XX' % (seq_cols, start)
end = start + len(fields[1])
seq_cols = slice(start, end)
del start, end
#Append the sequence
seqs[i] += fields[1]
assert len(seqs[i]) == len(seqs[0])
if len(fields) == 3:
#This MAY be an old style file with a letter count...
try:
letters = int(fields[2])
except ValueError:
raise ValueError("Could not parse line, bad sequence number:\n%s" % line)
if len(seqs[i].replace("-", "")) != letters:
raise ValueError("Could not parse line, invalid sequence number:\n%s" % line)
#Read in the next line
line = handle.readline()
#There should now be a consensus line
if consensus:
assert line[0] == " "
assert seq_cols is not None
consensus += line[seq_cols]
assert len(consensus) == len(seqs[0])
assert not line[:seq_cols.start].strip()
assert not line[seq_cols.stop:].strip()
#Read in the next line
line = handle.readline()
assert len(ids) == len(seqs)
if len(seqs) == 0 or len(seqs[0]) == 0:
raise StopIteration
if self.records_per_alignment is not None \
and self.records_per_alignment != len(ids):
raise ValueError("Found %i records in this alignment, told to expect %i"
% (len(ids), self.records_per_alignment))
records = (SeqRecord(Seq(s, self.alphabet), id=i, description=i)
for (i, s) in zip(ids, seqs))
alignment = MultipleSeqAlignment(records, self.alphabet)
#TODO - Handle alignment annotation better, for now
#mimic the old parser in Bio.Clustalw
if version:
alignment._version = version
if consensus:
alignment_length = len(seqs[0])
assert len(consensus) == alignment_length, \
"Alignment length is %i, consensus length is %i, '%s'" \
% (alignment_length, len(consensus), consensus)
alignment._star_info = consensus
return alignment
