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# Copyright 2022 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.Align support for hhr files generated by HHsearch or HHblits in HH-suite.
This module provides support for output in the hhr file format generated by
HHsearch or HHblits in HH-suite.
You are expected to use this module via the Bio.Align functions.
"""
from Bio.Align import Alignment
from Bio.Align import interfaces
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
class AlignmentIterator(interfaces.AlignmentIterator):
"""Alignment iterator for hhr output files generated by HHsearch or HHblits.
HHsearch and HHblits are part of the HH-suite of programs for Hidden Markov
Models. An output files in the hhr format contains multiple pairwise
alignments for a single query sequence.
"""
fmt = "hhr"
def _read_header(self, stream):
metadata = {}
for line in stream:
line = line.strip()
if line == "":
break
key, value = line.split(None, 1)
if key == "Query":
self.query_name = value
elif key == "Match_columns":
metadata[key] = int(value)
elif key == "No_of_seqs":
value1, value2 = value.split(" out of ")
metadata[key] = (int(value1), int(value2))
elif key in ("Neff", "Template_Neff"):
metadata[key] = float(value)
elif key == "Searched_HMMs":
metadata[key] = int(value)
elif key == "Date":
metadata["Rundate"] = value
elif key == "Command":
metadata["Command line"] = value
else:
raise ValueError("Unknown key '%s'" % key)
self.metadata = metadata
try:
line = next(stream)
except StopIteration:
raise ValueError("Truncated file.") from None
assert line.split() == [
"No",
"Hit",
"Prob",
"E-value",
"P-value",
"Score",
"SS",
"Cols",
"Query",
"HMM",
"Template",
"HMM",
]
counter = 0
for line in stream:
if line.strip() == "":
break
counter += 1
word, _ = line.split(None, 1)
assert int(word) == counter
self._length = counter
self._counter = 0
def _read_next_alignment(self, stream):
def create_alignment():
n = len(target_sequence)
assert len(query_sequence) == n
if n == 0:
return
coordinates = Alignment.infer_coordinates([target_sequence, query_sequence])
coordinates[0, :] += target_start
coordinates[1, :] += query_start
sequence = {query_start: query_sequence.replace("-", "")}
query_seq = Seq(sequence, length=query_length)
query = SeqRecord(query_seq, id=self.query_name)
sequence = {target_start: target_sequence.replace("-", "")}
target_seq = Seq(sequence, length=target_length)
target_annotations = {
"hmm_name": hmm_name,
"hmm_description": hmm_description,
}
target = SeqRecord(
target_seq, id=target_name, annotations=target_annotations
)
fmt = f"{' ' * target_start}%-{target_length - target_start}s"
target.letter_annotations["Consensus"] = fmt % target_consensus.replace(
"-", ""
)
target.letter_annotations["ss_pred"] = fmt % target_ss_pred.replace("-", "")
target.letter_annotations["ss_dssp"] = fmt % target_ss_dssp.replace("-", "")
target.letter_annotations["Confidence"] = fmt % confidence.replace(" ", "")
fmt = f"{' ' * query_start}%-{query_length - query_start}s"
query.letter_annotations["Consensus"] = fmt % query_consensus.replace(
"-", ""
)
query.letter_annotations["ss_pred"] = fmt % query_ss_pred.replace("-", "")
records = [target, query]
alignment = Alignment(records, coordinates=coordinates)
alignment.annotations = alignment_annotations
alignment.column_annotations = {}
alignment.column_annotations["column score"] = column_score
return alignment
query_start = None
query_sequence = ""
query_consensus = ""
query_ss_pred = ""
target_start = None
target_sequence = ""
target_consensus = ""
target_ss_pred = ""
target_ss_dssp = ""
column_score = ""
confidence = ""
for line in stream:
line = line.rstrip()
if not line:
pass
elif line.startswith(">"):
hmm_name, hmm_description = line[1:].split(None, 1)
line = next(stream)
words = line.split()
alignment_annotations = {}
for word in words:
key, value = word.split("=")
if key == "Aligned_cols":
continue # can be obtained from coordinates
if key == "Identities":
value = value.rstrip("%")
value = float(value)
alignment_annotations[key] = value
elif line == "Done!":
try:
next(stream)
except StopIteration:
pass
else:
raise ValueError(
"Found additional data after 'Done!'; corrupt file?"
)
elif line.startswith(" "):
column_score += line.strip()
elif line.startswith("No "):
counter = self._counter
self._counter += 1
key, value = line.split()
assert int(value) == self._counter
if self._counter > self._length:
raise ValueError(
"Expected %d alignments, found %d"
% (self._length, self._counter)
)
if counter > 0:
return create_alignment()
elif line.startswith("Confidence"):
key, value = line.split(None, 1)
confidence += value
elif line.startswith("Q ss_pred "):
key, value = line.rsplit(None, 1)
query_ss_pred += value
elif line.startswith("Q Consensus "):
key1, key2, start, consensus, end, total = line.split()
start = int(start) - 1
end = int(end)
assert total.startswith("(")
assert total.endswith(")")
total = int(total[1:-1])
query_consensus += consensus
elif line.startswith("Q "):
key1, key2, start, sequence, end, total = line.split()
assert self.query_name.startswith(key2)
start = int(start) - 1
end = int(end)
assert total.startswith("(")
assert total.endswith(")")
query_length = int(total[1:-1])
assert query_length == self.metadata["Match_columns"]
if query_start is None:
query_start = start
query_sequence += sequence
elif line.startswith("T ss_pred "):
key, value = line.rsplit(None, 1)
target_ss_pred += value
elif line.startswith("T ss_dssp "):
key, value = line.rsplit(None, 1)
target_ss_dssp += value
elif line.startswith("T Consensus "):
key1, key2, start, consensus, end, total = line.split()
start = int(start) - 1
end = int(end)
assert total.startswith("(")
assert total.endswith(")")
total = int(total[1:-1])
target_consensus += consensus
elif line.startswith("T "):
key, name, start, sequence, end, total = line.split()
assert key == "T"
target_name = name
start = int(start) - 1
end = int(end)
assert total.startswith("(")
assert total.endswith(")")
target_length = int(total[1:-1])
if target_start is None:
target_start = start
target_sequence += sequence
else:
raise ValueError("Failed to parse line '%s...'" % line[:30])
alignment = create_alignment()
length = self._length
counter = self._counter
if length == counter:
self._close()
del self._counter
if alignment is None and length > 0:
raise ValueError("Expected %d alignments, found %d" % (length, counter))
return alignment
def __len__(self):
return self._length
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