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# Copyright 2023 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 the "chain" pairwise alignment format.
As described by UCSC, a chain file stores a series of pairwise alignments in a
single file. Typically they are used for genome to genome alignments. Chain
files store the lengths of the aligned segments, alignment gaps, and alignment
scores, but do not store the aligned sequences.
See https://genome.ucsc.edu/goldenPath/help/chain.html.
You are expected to use this module via the Bio.Align functions.
Coordinates in the chain file format are defined in terms of zero-based start
positions (like Python) and aligning region sizes.
"""
import numpy as np
from Bio.Align import Alignment
from Bio.Align import interfaces
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
class AlignmentWriter(interfaces.AlignmentWriter):
"""Alignment file writer for the UCSC chain file format."""
fmt = "chain"
def format_alignment(self, alignment):
"""Return a string with one alignment formatted as a chain block."""
if not isinstance(alignment, Alignment):
raise TypeError("Expected an Alignment object")
coordinates = alignment.coordinates
if not coordinates.size: # alignment consists of gaps only
return ""
target, query = alignment.sequences
try:
qName = query.id
except AttributeError:
qName = "query"
try:
query = query.seq
except AttributeError:
pass
try:
tName = target.id
except AttributeError:
tName = "target"
try:
target = target.seq
except AttributeError:
pass
tSize = len(target)
qSize = len(query)
lines = []
try:
score = alignment.score
except AttributeError:
score = 0
if coordinates[0, 0] > coordinates[0, -1]:
tStrand = "-"
coordinates = coordinates.copy()
coordinates[0, :] = tSize - coordinates[0, :]
else:
tStrand = "+"
if coordinates[1, 0] > coordinates[1, -1]:
qStrand = "-"
coordinates = coordinates.copy()
coordinates[1, :] = qSize - coordinates[1, :]
else:
qStrand = "+"
tStart = coordinates[0, 0]
tEnd = coordinates[0, -1]
qStart = coordinates[1, 0]
qEnd = coordinates[1, -1]
try:
chainID = alignment.annotations["id"]
except (AttributeError, KeyError):
line = f"chain {score:g} {tName} {tSize} {tStrand} {tStart} {tEnd} {qName} {qSize} {qStrand} {qStart} {qEnd}"
else:
line = f"chain {score:g} {tName} {tSize} {tStrand} {tStart} {tEnd} {qName} {qSize} {qStrand} {qStart} {qEnd} {chainID}"
lines.append(line)
# variable names follow those in the UCSC chain file format description
tStart, qStart = coordinates[:, 0]
step = 0
qGap = 0
tGap = 0
for tEnd, qEnd in coordinates[:, 1:].transpose():
if tStart == tEnd:
if tGap > 0:
qGap = qEnd - qStart
line = f"{step}\t{tGap}\t{qGap}"
lines.append(line)
step = 0
tGap = 0
qGap = 0
elif qGap > 0:
line = f"{step}\t{tGap}\t{qGap}"
lines.append(line)
step = 0
qGap = qEnd - qStart
else:
qGap = qEnd - qStart
qStart = qEnd
elif qStart == qEnd:
if qGap > 0:
tGap = tEnd - tStart
line = f"{step}\t{tGap}\t{qGap}"
lines.append(line)
step = 0
tGap = 0
qGap = 0
elif tGap > 0:
line = f"{step}\t{tGap}\t{qGap}"
lines.append(line)
step = 0
tGap = tEnd - tStart
else:
tGap = tEnd - tStart
tStart = tEnd
else:
if step == 0:
tStep = tEnd - tStart
qStep = qEnd - qStart
if tGap == 0 and qGap == 0:
step = tStep
else:
line = f"{tStep}\t{tGap}\t{qGap}"
lines.append(line)
tGap = 0
qGap = 0
else:
line = f"{step}\t{tGap}\t{qGap}"
lines.append(line)
tStep = tEnd - tStart
qStep = qEnd - qStart
step = tStep
tGap = 0
qGap = 0
if tStep != qStep:
raise ValueError(
f"Expected equal step size in target and query (found {tStep} and {qStep})"
)
tStart = tEnd
qStart = qEnd
if tGap > 0 or qGap > 0:
line = f"0\t{tGap}\t{qGap}"
lines.append(line)
line = f"{step}"
lines.append(line)
line = ""
lines.append(line)
block = "\n".join(lines) + "\n"
return block
class AlignmentIterator(interfaces.AlignmentIterator):
"""Alignment iterator for UCSC chain files.
Each chain block in the file contains one pairwise alignment, which are
loaded and returned incrementally. The alignment score is scored as an
attribute of the alignment; the ID is stored under the key "id" in the
dictionary referred to by the annotations attribute of the alignment.
"""
fmt = "chain"
def _read_header(self, stream):
try:
self._line = next(stream)
except StopIteration:
self._line = None
def _read_next_alignment(self, stream):
if self._line is None:
return
line = self._line
self._line = None
words = line.split()
if len(words) == 12:
chainID = None
elif len(words) == 13:
chainID = words[12]
else:
raise ValueError(
"expected line with 12 or 13 columns at the beginning of a chain block"
)
if words[0] != "chain":
raise ValueError(
"expected first line of chain block to start with 'chain '"
)
score = float(words[1])
tName = words[2]
tSize = int(words[3])
tStrand = words[4]
tStart = int(words[5])
tEnd = int(words[6])
qName = words[7]
qSize = int(words[8])
qStrand = words[9]
qStart = int(words[10])
qEnd = int(words[11])
qPosition = 0
tPosition = 0
qStarts = [qPosition]
tStarts = [tPosition]
for line in stream:
words = line.split()
if words[0] == "chain":
self._line = line
break
step = int(words[0])
qPosition += step
tPosition += step
qStarts.append(qPosition)
tStarts.append(tPosition)
if len(words) == 1:
break
tGap = int(words[1])
qGap = int(words[2])
if tGap > 0:
tPosition += tGap
qStarts.append(qPosition)
tStarts.append(tPosition)
if qGap > 0:
qPosition += qGap
qStarts.append(qPosition)
tStarts.append(tPosition)
target_sequence = Seq(None, length=tSize)
query_sequence = Seq(None, length=qSize)
target_record = SeqRecord(target_sequence, id=tName, description="")
query_record = SeqRecord(query_sequence, id=qName, description="")
records = [target_record, query_record]
coordinates = np.array([tStarts, qStarts])
coordinates[0, :] += tStart
coordinates[1, :] += qStart
if tStrand == "+":
pass
elif tStrand == "-":
coordinates[0, :] = tSize - coordinates[0, :]
else:
raise ValueError(f"tStrand should be '+' or '-' (found '{tStrand}')")
if qStrand == "+":
pass
elif qStrand == "-":
coordinates[1, :] = qSize - coordinates[1, :]
else:
raise ValueError(f"qStrand should be '+' or '-' (found '{qStrand}')")
alignment = Alignment(records, coordinates)
alignment.score = score
if chainID is not None:
alignment.annotations = {"id": chainID}
# There is supposed to be a blank line between chain blocks, but some
# tools (e.g. pslToChain) do not include such a blank line in their
# output.
try:
line = next(stream)
if line.strip() == "":
line = next(stream)
self._line = line
except StopIteration:
self._line = None
return alignment
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