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# Copyright 2006-2016 by Peter Cock. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.AlignIO support for "clustal" output from CLUSTAL W and other tools.
You are expected to use this module via the Bio.AlignIO functions (or the
Bio.SeqIO functions if you want to work directly with the gapped sequences).
"""
from __future__ import print_function
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Align import MultipleSeqAlignment
from .Interfaces import AlignmentIterator, SequentialAlignmentWriter
class ClustalWriter(SequentialAlignmentWriter):
"""Clustalw alignment writer."""
def write_alignment(self, alignment):
"""Use this to write (another) single alignment to an open file."""
if len(alignment) == 0:
raise ValueError("Must have at least one sequence")
if alignment.get_alignment_length() == 0:
# This doubles as a check for an alignment object
raise ValueError("Non-empty sequences are required")
# Old versions of the parser in Bio.Clustalw used a ._version property,
try:
version = str(alignment._version)
except AttributeError:
version = ""
if not version:
version = '1.81'
if version.startswith("2."):
# e.g. 2.0.x
output = "CLUSTAL %s multiple sequence alignment\n\n\n" % version
else:
# e.g. 1.81 or 1.83
output = "CLUSTAL X (%s) multiple sequence alignment\n\n\n" % version
cur_char = 0
max_length = len(alignment[0])
if max_length <= 0:
raise ValueError("Non-empty sequences are required")
# keep displaying sequences until we reach the end
while cur_char != max_length:
# calculate the number of sequences to show, which will
# be less if we are at the end of the sequence
if (cur_char + 50) > max_length:
show_num = max_length - cur_char
else:
show_num = 50
# go through all of the records and print out the sequences
# when we output, we do a nice 80 column output, although this
# may result in truncation of the ids.
for record in alignment:
# Make sure we don't get any spaces in the record
# identifier when output in the file by replacing
# them with underscores:
line = record.id[0:30].replace(" ", "_").ljust(36)
line += str(record.seq[cur_char:(cur_char + show_num)])
output += line + "\n"
# now we need to print out the star info, if we've got it
# This was stored by Bio.Clustalw using a ._star_info property.
if hasattr(alignment, "_star_info") and alignment._star_info != '':
output += (" " * 36) + \
alignment._star_info[cur_char:(cur_char + show_num)] + "\n"
output += "\n"
cur_char += show_num
# Want a trailing blank new line in case the output is concatenated
self.handle.write(output + "\n")
class ClustalIterator(AlignmentIterator):
"""Clustalw alignment iterator."""
_header = None # for caching lines between __next__ calls
def __next__(self):
handle = self.handle
if self._header is None:
line = handle.readline()
else:
# Header we saved from when we were parsing
# the previous alignment.
line = self._header
self._header = None
if not line:
raise StopIteration
# Whitelisted headers we know about
known_headers = ['CLUSTAL', 'PROBCONS', 'MUSCLE', 'MSAPROBS', 'Kalign']
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
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