def to_generic(self, alphabet):
"""Retrieve generic alignment object for the given alignment.
Instead of the tuples, this returns a MultipleSeqAlignment object
from SAP.Bio.Align, through which you can manipulate and query
the object.
alphabet is the specified alphabet for the sequences in the code (for
example IUPAC.IUPACProtein).
Thanks to James Casbon for the code.
"""
#TODO - Switch to new Bio.Align.MultipleSeqAlignment class?
seq_parts = []
seq_names = []
parse_number = 0
n = 0
for name, start, seq, end in self.alignment:
if name == 'QUERY': # QUERY is the first in each alignment block
parse_number += 1
n = 0
if parse_number == 1: # create on first_parse, append on all others
seq_parts.append(seq)
seq_names.append(name)
else:
seq_parts[n] += seq
n += 1
generic = MultipleSeqAlignment([], alphabet)
for (name, seq) in zip(seq_names, seq_parts):
generic.append(SeqRecord(Seq(seq, alphabet), name))
return generic
def __getitem__(self, index, alphabet=None):
"""Return a CodonAlignment object for single indexing
"""
if isinstance(index, int):
return self._records[index]
elif isinstance(index, slice):
return CodonAlignment(self._records[index], self._alphabet)
elif len(index) != 2:
raise TypeError("Invalid index type.")
# Handle double indexing
row_index, col_index = index
if isinstance(row_index, int):
return self._records[row_index][col_index]
elif isinstance(col_index, int):
return "".join(str(rec[col_index]) for rec in \
self._records[row_index])
else:
if alphabet is None:
from SAP.Bio.Alphabet import generic_nucleotide
return MultipleSeqAlignment((rec[col_index] for rec in \
self._records[row_index]),
generic_nucleotide)
else:
return MultipleSeqAlignment((rec[col_index] for rec in \
self._records[row_index]),
generic_nucleotide)
def to_generic(self, alphabet):
"""Retrieve generic alignment object for the given alignment.
Instead of the tuples, this returns a MultipleSeqAlignment object
from SAP.Bio.Align, through which you can manipulate and query
the object.
alphabet is the specified alphabet for the sequences in the code (for
example IUPAC.IUPACProtein).
Thanks to James Casbon for the code.
"""
#TODO - Switch to new Bio.Align.MultipleSeqAlignment class?
seq_parts = []
seq_names = []
parse_number = 0
n = 0
for name, start, seq, end in self.alignment:
if name == 'QUERY': # QUERY is the first in each alignment block
parse_number += 1
n = 0
if parse_number == 1: # create on first_parse, append on all others
seq_parts.append(seq)
seq_names.append(name)
else:
seq_parts[n] += seq
n += 1
generic = MultipleSeqAlignment([], alphabet)
for (name, seq) in zip(seq_names, seq_parts):
generic.append(SeqRecord(Seq(seq, alphabet), name))
return generic
def _aln_get(self):
if self.query is None and self.hit is None:
return None
elif self.hit is None:
return MultipleSeqAlignment([self.query], self.alphabet)
elif self.query is None:
return MultipleSeqAlignment([self.hit], self.alphabet)
else:
return MultipleSeqAlignment([self.query, self.hit], self.alphabet)
def __init__(self, records='', name=None, alphabet=default_codon_alphabet):
MultipleSeqAlignment.__init__(self, records, alphabet=alphabet)
# check the type of the alignment to be nucleotide
for rec in self:
if not isinstance(rec.seq, CodonSeq):
raise TypeError("CodonSeq object are expected in each "
"SeqRecord in CodonAlignment")
assert self.get_alignment_length() % 3 == 0, \
"Alignment length is not a triple number"
def __init__(self, records='', name=None, alphabet=default_codon_alphabet):
MultipleSeqAlignment.__init__(self, records, alphabet=alphabet)
# check the type of the alignment to be nucleotide
for rec in self:
if not isinstance(rec.seq, CodonSeq):
raise TypeError("CodonSeq object are expected in each "
"SeqRecord in CodonAlignment")
assert self.get_alignment_length() % 3 == 0, \
"Alignment length is not a triple number"
def to_alignment(self):
"""Construct an alignment from the aligned sequences in this tree."""
def is_aligned_seq(elem):
if isinstance(elem, Sequence) and elem.mol_seq.is_aligned:
return True
return False
seqs = self._filter_search(is_aligned_seq, 'preorder', True)
try:
first_seq = next(seqs)
except StopIteration:
# No aligned sequences were found --> empty MSA
return MultipleSeqAlignment([])
msa = MultipleSeqAlignment([first_seq.to_seqrecord()],
first_seq.get_alphabet())
msa.extend(seq.to_seqrecord() for seq in seqs)
return msa
def NexusIterator(handle, seq_count=None):
"""Returns SeqRecord objects from a Nexus file.
Thus uses the Bio.Nexus module to do the hard work.
You are expected to call this function via Bio.SeqIO or Bio.AlignIO
(and not use it directly).
NOTE - We only expect ONE alignment matrix per Nexus file,
meaning this iterator will only yield one MultipleSeqAlignment.
"""
n = Nexus.Nexus(handle)
if not n.matrix:
#No alignment found
raise StopIteration
#Bio.Nexus deals with duplicated names by adding a '.copy' suffix.
#The original names and the modified names are kept in these two lists:
assert len(n.unaltered_taxlabels) == len(n.taxlabels)
if seq_count and seq_count != len(n.unaltered_taxlabels):
raise ValueError("Found %i sequences, but seq_count=%i"
% (len(n.unaltered_taxlabels), seq_count))
#ToDo - Can we extract any annotation too?
records = (SeqRecord(n.matrix[new_name], id=new_name,
name=old_name, description="")
for old_name, new_name
in zip(n.unaltered_taxlabels, n.taxlabels))
#All done
yield MultipleSeqAlignment(records, n.alphabet)
def mult_align(sum_dict, align_dict):
"""Returns a biopython multiple alignment instance (MultipleSeqAlignment)"""
mult_align_dict = {}
for j in align_dict.abs(1).pos_align_dict:
mult_align_dict[j] = ''
for i in range(1, len(align_dict)+1):
# loop on positions
for j in align_dict.abs(i).pos_align_dict:
# loop within a position
mult_align_dict[j] += align_dict.abs(i).pos_align_dict[j].aa
alpha = Alphabet.Gapped(Alphabet.IUPAC.extended_protein)
fssp_align = MultipleSeqAlignment([], alphabet=alpha)
for i in sorted(mult_align_dict):
fssp_align.append(SeqRecord(Seq(mult_align_dict[i], alpha),
sum_dict[i].pdb2+sum_dict[i].chain2))
return fssp_align
def toMultipleSeqAlignment(self):
"""Return a MultipleSeqAlignment containing all the
SeqRecord in the CodonAlignment using Seq to store
sequences
"""
alignments = [SeqRecord(rec.seq.toSeq(), id=rec.id) for \
rec in self._records]
return MultipleSeqAlignment(alignments)
def to_alignment(self):
"""Construct an alignment from the aligned sequences in this tree."""
def is_aligned_seq(elem):
if isinstance(elem, Sequence) and elem.mol_seq.is_aligned:
return True
return False
seqs = self._filter_search(is_aligned_seq, 'preorder', True)
try:
first_seq = next(seqs)
except StopIteration:
# No aligned sequences were found --> empty MSA
return MultipleSeqAlignment([])
msa = MultipleSeqAlignment([first_seq.to_seqrecord()],
first_seq.get_alphabet())
msa.extend(seq.to_seqrecord() for seq in seqs)
return msa
def write(sequences, handle, format):
"""Write complete set of sequences to a file.
- sequences - A list (or iterator) of SeqRecord objects, or (if using
Biopython 1.54 or later) a single SeqRecord.
- handle - File handle object to write to, or filename as string
(note older versions of Biopython only took a handle).
- format - lower case string describing the file format to write.
You should close the handle after calling this function.
Returns the number of records written (as an integer).
"""
from SAP.Bio import AlignIO
#Try and give helpful error messages:
if not isinstance(format, basestring):
raise TypeError("Need a string for the file format (lower case)")
if not format:
raise ValueError("Format required (lower case string)")
if format != format.lower():
raise ValueError("Format string '%s' should be lower case" % format)
if isinstance(sequences, SeqRecord):
#This raised an exception in order version of Biopython
sequences = [sequences]
if format in _BinaryFormats:
mode = 'wb'
else:
mode = 'w'
with as_handle(handle, mode) as fp:
#Map the file format to a writer class
if format in _FormatToWriter:
writer_class = _FormatToWriter[format]
count = writer_class(fp).write_file(sequences)
elif format in AlignIO._FormatToWriter:
#Try and turn all the records into a single alignment,
#and write that using Bio.AlignIO
alignment = MultipleSeqAlignment(sequences)
alignment_count = AlignIO.write([alignment], fp, format)
assert alignment_count == 1, \
"Internal error - the underlying writer " \
" should have returned 1, not %s" % repr(alignment_count)
count = len(alignment)
del alignment_count, alignment
elif format in _FormatToIterator or format in AlignIO._FormatToIterator:
raise ValueError(
"Reading format '%s' is supported, but not writing" % format)
else:
raise ValueError("Unknown format '%s'" % format)
assert isinstance(count, int), "Internal error - the underlying %s " \
"writer should have returned the record count, not %s" \
% (format, repr(count))
return count
def mult_align(sum_dict, align_dict):
"""Returns a biopython multiple alignment instance (MultipleSeqAlignment)"""
mult_align_dict = {}
for j in align_dict.abs(1).pos_align_dict:
mult_align_dict[j] = ''
for i in range(1, len(align_dict) + 1):
# loop on positions
for j in align_dict.abs(i).pos_align_dict:
# loop within a position
mult_align_dict[j] += align_dict.abs(i).pos_align_dict[j].aa
alpha = Alphabet.Gapped(Alphabet.IUPAC.extended_protein)
fssp_align = MultipleSeqAlignment([], alphabet=alpha)
for i in sorted(mult_align_dict):
fssp_align.append(
SeqRecord(Seq(mult_align_dict[i], alpha),
sum_dict[i].pdb2 + sum_dict[i].chain2))
return fssp_align
def _SeqIO_to_alignment_iterator(handle,
format,
alphabet=None,
seq_count=None):
"""Uses Bio.SeqIO to create an MultipleSeqAlignment iterator (PRIVATE).
Arguments:
- handle - handle to the file.
- format - string describing the file format.
- alphabet - optional Alphabet object, useful when the sequence type
cannot be automatically inferred from the file itself
(e.g. fasta, phylip, clustal)
- seq_count - Optional integer, number of sequences expected in each
alignment. Recommended for fasta format files.
If count is omitted (default) then all the sequences in the file are
combined into a single MultipleSeqAlignment.
"""
from SAP.Bio import SeqIO
assert format in SeqIO._FormatToIterator
if seq_count:
#Use the count to split the records into batches.
seq_record_iterator = SeqIO.parse(handle, format, alphabet)
records = []
for record in seq_record_iterator:
records.append(record)
if len(records) == seq_count:
yield MultipleSeqAlignment(records, alphabet)
records = []
if len(records) > 0:
raise ValueError("Check seq_count argument, not enough sequences?")
else:
#Must assume that there is a single alignment using all
#the SeqRecord objects:
records = list(SeqIO.parse(handle, format, alphabet))
if records:
yield MultipleSeqAlignment(records, alphabet)
raise StopIteration
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
line = line.strip()
parts = [x for x in line.split() if x]
if len(parts) != 2:
raise ValueError("First line should have two integers")
try:
number_of_seqs = int(parts[0])
length_of_seqs = int(parts[1])
except ValueError:
raise ValueError("First line should have two integers")
assert self._is_header(line)
if self.records_per_alignment is not None \
and self.records_per_alignment != number_of_seqs:
raise ValueError(
"Found %i records in this alignment, told to expect %i" %
(number_of_seqs, self.records_per_alignment))
ids = []
seqs = []
# By default, expects STRICT truncation / padding to 10 characters.
# Does not require any whitespace between name and seq.
for i in range(number_of_seqs):
line = handle.readline().rstrip()
sequence_id, s = self._split_id(line)
ids.append(sequence_id)
while len(s) < length_of_seqs:
# The sequence may be split into multiple lines
line = handle.readline().strip()
if not line:
break
if line == "":
continue
s = "".join([s, line.strip().replace(" ", "")])
if len(s) > length_of_seqs:
raise ValueError(
"Found a record of length %i, should be %i" %
(len(s), length_of_seqs))
if "." in s:
raise ValueError(
"PHYLIP format no longer allows dots in sequence")
seqs.append(s)
while True:
# Find other alignments in the file
line = handle.readline()
if not line:
break
if self._is_header(line):
self._header = line
break
records = (SeqRecord(Seq(s, self.alphabet),
id=i,
name=i,
description=i) for (i, s) in zip(ids, seqs))
return MultipleSeqAlignment(records, self.alphabet)
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
line = line.strip()
parts = [x for x in line.split() if x]
if len(parts) != 2:
raise ValueError("First line should have two integers")
try:
number_of_seqs = int(parts[0])
length_of_seqs = int(parts[1])
except ValueError:
raise ValueError("First line should have two integers")
assert self._is_header(line)
if self.records_per_alignment is not None \
and self.records_per_alignment != number_of_seqs:
raise ValueError(
"Found %i records in this alignment, told to expect %i" %
(number_of_seqs, self.records_per_alignment))
ids = []
seqs = []
# By default, expects STRICT truncation / padding to 10 characters.
# Does not require any whitespace between name and seq.
for i in range(number_of_seqs):
line = handle.readline().rstrip()
sequence_id, s = self._split_id(line)
ids.append(sequence_id)
if "." in s:
raise ValueError(
"PHYLIP format no longer allows dots in sequence")
seqs.append([s])
#Look for further blocks
line = ""
while True:
#Skip any blank lines between blocks...
while "" == line.strip():
line = handle.readline()
if not line:
break # end of file
if not line:
break # end of file
if self._is_header(line):
#Looks like the start of a concatenated alignment
self._header = line
break
#print "New block..."
for i in range(number_of_seqs):
s = line.strip().replace(" ", "")
if "." in s:
raise ValueError(
"PHYLIP format no longer allows dots in sequence")
seqs[i].append(s)
line = handle.readline()
if (not line) and i + 1 < number_of_seqs:
raise ValueError("End of file mid-block")
if not line:
break # end of file
records = (SeqRecord(Seq("".join(s), self.alphabet),
id=i,
name=i,
description=i) for (i, s) in zip(ids, seqs))
return MultipleSeqAlignment(records, self.alphabet)
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):
try:
line = self._header
del self._header
except AttributeError:
line = self.handle.readline()
if not line:
#Empty file - just give up.
raise StopIteration
if not line.strip() == '# STOCKHOLM 1.0':
raise ValueError("Did not find STOCKHOLM header")
# Note: If this file follows the PFAM conventions, there should be
# a line containing the number of sequences, e.g. "#=GF SQ 67"
# We do not check for this - perhaps we should, and verify that
# if present it agrees with our parsing.
seqs = {}
ids = []
gs = {}
gr = {}
gf = {}
passed_end_alignment = False
while True:
line = self.handle.readline()
if not line:
break # end of file
line = line.strip() # remove trailing \n
if line == '# STOCKHOLM 1.0':
self._header = line
break
elif line == "//":
#The "//" line indicates the end of the alignment.
#There may still be more meta-data
passed_end_alignment = True
elif line == "":
#blank line, ignore
pass
elif line[0] != "#":
#Sequence
#Format: "<seqname> <sequence>"
assert not passed_end_alignment
parts = [x.strip() for x in line.split(" ", 1)]
if len(parts) != 2:
#This might be someone attempting to store a zero length sequence?
raise ValueError("Could not split line into identifier "
+ "and sequence:\n" + line)
id, seq = parts
if id not in ids:
ids.append(id)
seqs.setdefault(id, '')
seqs[id] += seq.replace(".", "-")
elif len(line) >= 5:
#Comment line or meta-data
if line[:5] == "#=GF ":
#Generic per-File annotation, free text
#Format: #=GF <feature> <free text>
feature, text = line[5:].strip().split(None, 1)
#Each feature key could be used more than once,
#so store the entries as a list of strings.
if feature not in gf:
gf[feature] = [text]
else:
gf[feature].append(text)
elif line[:5] == '#=GC ':
#Generic per-Column annotation, exactly 1 char per column
#Format: "#=GC <feature> <exactly 1 char per column>"
pass
elif line[:5] == '#=GS ':
#Generic per-Sequence annotation, free text
#Format: "#=GS <seqname> <feature> <free text>"
id, feature, text = line[5:].strip().split(None, 2)
#if id not in ids:
# ids.append(id)
if id not in gs:
gs[id] = {}
if feature not in gs[id]:
gs[id][feature] = [text]
else:
gs[id][feature].append(text)
elif line[:5] == "#=GR ":
#Generic per-Sequence AND per-Column markup
#Format: "#=GR <seqname> <feature> <exactly 1 char per column>"
id, feature, text = line[5:].strip().split(None, 2)
#if id not in ids:
# ids.append(id)
if id not in gr:
gr[id] = {}
if feature not in gr[id]:
gr[id][feature] = ""
gr[id][feature] += text.strip() # append to any previous entry
#TODO - Should we check the length matches the alignment length?
# For iterlaced sequences the GR data can be split over
# multiple lines
#Next line...
assert len(seqs) <= len(ids)
#assert len(gs) <= len(ids)
#assert len(gr) <= len(ids)
self.ids = ids
self.sequences = seqs
self.seq_annotation = gs
self.seq_col_annotation = gr
if ids and seqs:
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))
alignment_length = len(list(seqs.values())[0])
records = [] # Alignment obj will put them all in a list anyway
for id in ids:
seq = seqs[id]
if alignment_length != len(seq):
raise ValueError("Sequences have different lengths, or repeated identifier")
name, start, end = self._identifier_split(id)
record = SeqRecord(Seq(seq, self.alphabet),
id=id, name=name, description=id,
annotations={"accession": name})
#Accession will be overridden by _populate_meta_data if an explicit
#accession is provided:
record.annotations["accession"] = name
if start is not None:
record.annotations["start"] = start
if end is not None:
record.annotations["end"] = end
self._populate_meta_data(id, record)
records.append(record)
alignment = MultipleSeqAlignment(records, self.alphabet)
#TODO - Introduce an annotated alignment class?
#For now, store the annotation a new private property:
alignment._annotations = gr
return alignment
else:
raise StopIteration
def __next__(self):
try:
line = self._header
del self._header
except AttributeError:
line = self.handle.readline()
if not line:
# Empty file - just give up.
raise StopIteration
if not line.strip() == "# STOCKHOLM 1.0":
raise ValueError("Did not find STOCKHOLM header")
# Note: If this file follows the PFAM conventions, there should be
# a line containing the number of sequences, e.g. "#=GF SQ 67"
# We do not check for this - perhaps we should, and verify that
# if present it agrees with our parsing.
seqs = {}
ids = []
gs = {}
gr = {}
gf = {}
passed_end_alignment = False
while True:
line = self.handle.readline()
if not line:
break # end of file
line = line.strip() # remove trailing \n
if line == "# STOCKHOLM 1.0":
self._header = line
break
elif line == "//":
# The "//" line indicates the end of the alignment.
# There may still be more meta-data
passed_end_alignment = True
elif line == "":
# blank line, ignore
pass
elif line[0] != "#":
# Sequence
# Format: "<seqname> <sequence>"
assert not passed_end_alignment
parts = [x.strip() for x in line.split(" ", 1)]
if len(parts) != 2:
# This might be someone attempting to store a zero length sequence?
raise ValueError("Could not split line into identifier " + "and sequence:\n" + line)
id, seq = parts
if id not in ids:
ids.append(id)
seqs.setdefault(id, "")
seqs[id] += seq.replace(".", "-")
elif len(line) >= 5:
# Comment line or meta-data
if line[:5] == "#=GF ":
# Generic per-File annotation, free text
# Format: #=GF <feature> <free text>
feature, text = line[5:].strip().split(None, 1)
# Each feature key could be used more than once,
# so store the entries as a list of strings.
if feature not in gf:
gf[feature] = [text]
else:
gf[feature].append(text)
elif line[:5] == "#=GC ":
# Generic per-Column annotation, exactly 1 char per column
# Format: "#=GC <feature> <exactly 1 char per column>"
pass
elif line[:5] == "#=GS ":
# Generic per-Sequence annotation, free text
# Format: "#=GS <seqname> <feature> <free text>"
id, feature, text = line[5:].strip().split(None, 2)
# if id not in ids:
# ids.append(id)
if id not in gs:
gs[id] = {}
if feature not in gs[id]:
gs[id][feature] = [text]
else:
gs[id][feature].append(text)
elif line[:5] == "#=GR ":
# Generic per-Sequence AND per-Column markup
# Format: "#=GR <seqname> <feature> <exactly 1 char per column>"
id, feature, text = line[5:].strip().split(None, 2)
# if id not in ids:
# ids.append(id)
if id not in gr:
gr[id] = {}
if feature not in gr[id]:
gr[id][feature] = ""
gr[id][feature] += text.strip() # append to any previous entry
# TODO - Should we check the length matches the alignment length?
# For iterlaced sequences the GR data can be split over
# multiple lines
# Next line...
assert len(seqs) <= len(ids)
# assert len(gs) <= len(ids)
# assert len(gr) <= len(ids)
self.ids = ids
self.sequences = seqs
self.seq_annotation = gs
self.seq_col_annotation = gr
if ids and seqs:
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)
)
alignment_length = len(list(seqs.values())[0])
records = [] # Alignment obj will put them all in a list anyway
for id in ids:
seq = seqs[id]
if alignment_length != len(seq):
raise ValueError("Sequences have different lengths, or repeated identifier")
name, start, end = self._identifier_split(id)
record = SeqRecord(
Seq(seq, self.alphabet), id=id, name=name, description=id, annotations={"accession": name}
)
# Accession will be overridden by _populate_meta_data if an explicit
# accession is provided:
record.annotations["accession"] = name
if start is not None:
record.annotations["start"] = start
if end is not None:
record.annotations["end"] = end
self._populate_meta_data(id, record)
records.append(record)
alignment = MultipleSeqAlignment(records, self.alphabet)
# TODO - Introduce an annotated alignment class?
# For now, store the annotation a new private property:
alignment._annotations = gr
return alignment
else:
raise StopIteration
def build_hsp():
if not query_tags and not match_tags:
raise ValueError("No data for query %r, match %r"
% (query_id, match_id))
assert query_tags, query_tags
assert match_tags, match_tags
evalue = align_tags.get("fa_expect", None)
q = "?" # Just for printing len(q) in debug below
m = "?" # Just for printing len(m) in debug below
tool = global_tags.get("tool", "").upper()
try:
q = _extract_alignment_region(query_seq, query_tags)
if tool in ["TFASTX"] and len(match_seq) == len(q):
m = match_seq
#Quick hack until I can work out how -, * and / characters
#and the apparent mix of aa and bp coordinates works.
else:
m = _extract_alignment_region(match_seq, match_tags)
assert len(q) == len(m)
except AssertionError as err:
print("Darn... amino acids vs nucleotide coordinates?")
print(tool)
print(query_seq)
print(query_tags)
print("%s %i" % (q, len(q)))
print(match_seq)
print(match_tags)
print("%s %i" % (m, len(m)))
print(handle.name)
raise err
assert alphabet is not None
alignment = MultipleSeqAlignment([], alphabet)
#TODO - Introduce an annotated alignment class?
#For now, store the annotation a new private property:
alignment._annotations = {}
#Want to record both the query header tags, and the alignment tags.
for key, value in header_tags.items():
alignment._annotations[key] = value
for key, value in align_tags.items():
alignment._annotations[key] = value
#Query
#=====
record = SeqRecord(Seq(q, alphabet),
id=query_id,
name="query",
description=query_descr,
annotations={"original_length": int(query_tags["sq_len"])})
#TODO - handle start/end coordinates properly. Short term hack for now:
record._al_start = int(query_tags["al_start"])
record._al_stop = int(query_tags["al_stop"])
alignment.append(record)
#TODO - What if a specific alphabet has been requested?
#TODO - Use an IUPAC alphabet?
#TODO - Can FASTA output RNA?
if alphabet == single_letter_alphabet and "sq_type" in query_tags:
if query_tags["sq_type"] == "D":
record.seq.alphabet = generic_dna
elif query_tags["sq_type"] == "p":
record.seq.alphabet = generic_protein
if "-" in q:
if not hasattr(record.seq.alphabet, "gap_char"):
record.seq.alphabet = Gapped(record.seq.alphabet, "-")
#Match
#=====
record = SeqRecord(Seq(m, alphabet),
id=match_id,
name="match",
description=match_descr,
annotations={"original_length": int(match_tags["sq_len"])})
#TODO - handle start/end coordinates properly. Short term hack for now:
record._al_start = int(match_tags["al_start"])
record._al_stop = int(match_tags["al_stop"])
alignment.append(record)
#This is still a very crude way of dealing with the alphabet:
if alphabet == single_letter_alphabet and "sq_type" in match_tags:
if match_tags["sq_type"] == "D":
record.seq.alphabet = generic_dna
elif match_tags["sq_type"] == "p":
record.seq.alphabet = generic_protein
if "-" in m:
if not hasattr(record.seq.alphabet, "gap_char"):
record.seq.alphabet = Gapped(record.seq.alphabet, "-")
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
while line.rstrip() != "#=======================================":
line = handle.readline()
if not line:
raise StopIteration
length_of_seqs = None
number_of_seqs = None
ids = []
seqs = []
while line[0] == "#":
#Read in the rest of this alignment header,
#try and discover the number of records expected
#and their length
parts = line[1:].split(":", 1)
key = parts[0].lower().strip()
if key == "aligned_sequences":
number_of_seqs = int(parts[1].strip())
assert len(ids) == 0
# Should now expect the record identifiers...
for i in range(number_of_seqs):
line = handle.readline()
parts = line[1:].strip().split(":", 1)
assert i+1 == int(parts[0].strip())
ids.append(parts[1].strip())
assert len(ids) == number_of_seqs
if key == "length":
length_of_seqs = int(parts[1].strip())
#And read in another line...
line = handle.readline()
if number_of_seqs is None:
raise ValueError("Number of sequences missing!")
if length_of_seqs is None:
raise ValueError("Length of sequences missing!")
if self.records_per_alignment is not None \
and self.records_per_alignment != number_of_seqs:
raise ValueError("Found %i records in this alignment, told to expect %i"
% (number_of_seqs, self.records_per_alignment))
seqs = ["" for id in ids]
seq_starts = []
index = 0
#Parse the seqs
while line:
if len(line) > 21:
id_start = line[:21].strip().split(None, 1)
seq_end = line[21:].strip().split(None, 1)
if len(id_start) == 2 and len(seq_end) == 2:
#identifier, seq start position, seq, seq end position
#(an aligned seq is broken up into multiple lines)
id, start = id_start
seq, end = seq_end
if start == end:
#Special case, either a single letter is present,
#or no letters at all.
if seq.replace("-", "") == "":
start = int(start)
end = int(end)
else:
start = int(start) - 1
end = int(end)
else:
assert seq.replace("-", "") != "", repr(line)
start = int(start) - 1 # python counting
end = int(end)
#The identifier is truncated...
assert 0 <= index and index < number_of_seqs, \
"Expected index %i in range [0,%i)" \
% (index, number_of_seqs)
assert id == ids[index] or id == ids[index][:len(id)]
if len(seq_starts) == index:
#Record the start
seq_starts.append(start)
#Check the start...
if start == end:
assert seq.replace("-", "") == "", line
else:
assert start - seq_starts[index] == len(seqs[index].replace("-", "")), \
"Found %i chars so far for sequence %i (%s, %s), line says start %i:\n%s" \
% (len(seqs[index].replace("-", "")), index, id, repr(seqs[index]),
start, line)
seqs[index] += seq
#Check the end ...
assert end == seq_starts[index] + len(seqs[index].replace("-", "")), \
"Found %i chars so far for sequence %i (%s, %s, start=%i), file says end %i:\n%s" \
% (len(seqs[index].replace("-", "")), index, id, repr(seqs[index]),
seq_starts[index], end, line)
index += 1
if index >= number_of_seqs:
index = 0
else:
#just a start value, this is just alignment annotation (?)
#print "Skipping: " + line.rstrip()
pass
elif line.strip() == "":
#Just a spacer?
pass
else:
print(line)
assert False
line = handle.readline()
if line.rstrip() == "#---------------------------------------" \
or line.rstrip() == "#=======================================":
#End of alignment
self._header = line
break
assert index == 0
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 = []
for id, seq in zip(ids, seqs):
if len(seq) != length_of_seqs:
#EMBOSS 2.9.0 is known to use spaces instead of minus signs
#for leading gaps, and thus fails to parse. This old version
#is still used as of Dec 2008 behind the EBI SOAP webservice:
#http://www.ebi.ac.uk/Tools/webservices/wsdl/WSEmboss.wsdl
raise ValueError("Error parsing alignment - sequences of "
"different length? You could be using an "
"old version of EMBOSS.")
records.append(SeqRecord(Seq(seq, self.alphabet),
id=id, description=id))
return MultipleSeqAlignment(records, self.alphabet)
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 build_hsp():
if not query_tags and not match_tags:
raise ValueError("No data for query %r, match %r" %
(query_id, match_id))
assert query_tags, query_tags
assert match_tags, match_tags
evalue = align_tags.get("fa_expect", None)
q = "?" # Just for printing len(q) in debug below
m = "?" # Just for printing len(m) in debug below
tool = global_tags.get("tool", "").upper()
try:
q = _extract_alignment_region(query_seq, query_tags)
if tool in ["TFASTX"] and len(match_seq) == len(q):
m = match_seq
#Quick hack until I can work out how -, * and / characters
#and the apparent mix of aa and bp coordinates works.
else:
m = _extract_alignment_region(match_seq, match_tags)
assert len(q) == len(m)
except AssertionError as err:
print("Darn... amino acids vs nucleotide coordinates?")
print(tool)
print(query_seq)
print(query_tags)
print("%s %i" % (q, len(q)))
print(match_seq)
print(match_tags)
print("%s %i" % (m, len(m)))
print(handle.name)
raise err
assert alphabet is not None
alignment = MultipleSeqAlignment([], alphabet)
#TODO - Introduce an annotated alignment class?
#For now, store the annotation a new private property:
alignment._annotations = {}
#Want to record both the query header tags, and the alignment tags.
for key, value in header_tags.items():
alignment._annotations[key] = value
for key, value in align_tags.items():
alignment._annotations[key] = value
#Query
#=====
record = SeqRecord(
Seq(q, alphabet),
id=query_id,
name="query",
description=query_descr,
annotations={"original_length": int(query_tags["sq_len"])})
#TODO - handle start/end coordinates properly. Short term hack for now:
record._al_start = int(query_tags["al_start"])
record._al_stop = int(query_tags["al_stop"])
alignment.append(record)
#TODO - What if a specific alphabet has been requested?
#TODO - Use an IUPAC alphabet?
#TODO - Can FASTA output RNA?
if alphabet == single_letter_alphabet and "sq_type" in query_tags:
if query_tags["sq_type"] == "D":
record.seq.alphabet = generic_dna
elif query_tags["sq_type"] == "p":
record.seq.alphabet = generic_protein
if "-" in q:
if not hasattr(record.seq.alphabet, "gap_char"):
record.seq.alphabet = Gapped(record.seq.alphabet, "-")
#Match
#=====
record = SeqRecord(
Seq(m, alphabet),
id=match_id,
name="match",
description=match_descr,
annotations={"original_length": int(match_tags["sq_len"])})
#TODO - handle start/end coordinates properly. Short term hack for now:
record._al_start = int(match_tags["al_start"])
record._al_stop = int(match_tags["al_stop"])
alignment.append(record)
#This is still a very crude way of dealing with the alphabet:
if alphabet == single_letter_alphabet and "sq_type" in match_tags:
if match_tags["sq_type"] == "D":
record.seq.alphabet = generic_dna
elif match_tags["sq_type"] == "p":
record.seq.alphabet = generic_protein
if "-" in m:
if not hasattr(record.seq.alphabet, "gap_char"):
record.seq.alphabet = Gapped(record.seq.alphabet, "-")
return alignment
