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# Copyright 2008-2016 by Peter Cock. 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 "emboss" alignment output from EMBOSS tools.
This module contains a parser for the EMBOSS srspair/pair/simple file format,
for example from the needle, water, and stretcher tools.
"""
from Bio.Align import Alignment
from Bio.Align import interfaces
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
class AlignmentIterator(interfaces.AlignmentIterator):
"""Emboss alignment iterator.
For reading the (pairwise) alignments from EMBOSS tools in what they
call the "pairs" and "simple" formats.
"""
fmt = "EMBOSS"
def _read_header(self, stream):
line = stream.readline()
if not line:
raise ValueError("Empty file.")
if line.rstrip() != "########################################":
raise ValueError("Unexpected line: %s") % line
# assume srspair format (default) if not specified explicitly in
# the output file
self.metadata = {}
self.metadata["Align_format"] = "srspair"
commandline = None
for line in stream:
if line.rstrip() == "########################################":
break
if not line.startswith("# "):
raise ValueError("Unexpected line: %s") % line
if commandline is not None:
if line.startswith("# "):
commandline += " " + line[1:].strip()
continue
self.metadata["Command line"] = commandline
commandline = None
key, value = line[2:].split(":", 1)
if key == "Program":
self.metadata["Program"] = value.strip()
elif key == "Rundate":
self.metadata["Rundate"] = value.strip()
elif key == "Report_file":
self.metadata["Report_file"] = value.strip()
elif key == "Align_format":
self.metadata["Align_format"] = value.strip()
elif key == "Commandline":
commandline = value.strip()
def _read_next_alignment(self, stream):
number_of_sequences = None
annotations = {}
for line in stream:
line = line.rstrip("\r\n")
if not line:
continue
elif line.startswith("#---------------------------------------"):
# may appear between alignments
continue
elif line.startswith("#======================================="):
# found the alignment metadata start
identifiers = []
ncols = None
sequences = None
break
else:
raise ValueError("Unexpected line: %s" % line)
for line in stream:
line = line.rstrip("\r\n")
if line == "#=======================================":
# reached the end of alignment metadata
break
elif line.strip() == "#":
continue
elif not line.startswith("# "):
raise ValueError("Unexpected line: %s") % line
try:
key, value = line[2:].split(":", 1)
except ValueError:
# An equal sign is used for Longest_Identity,
# Longest_Similarity, Shortest_Identity, and
# Shortest_Similarity, which are included if command line
# argument -nobrief was used.
key, value = line[2:].split(" = ", 1)
if key == "Aligned_sequences":
number_of_sequences = int(value.strip())
assert len(identifiers) == 0
# Should now expect the record identifiers...
for i, line in enumerate(stream):
if not line.startswith("# "):
raise ValueError("Unexpected line: %s") % line
number, identifier = line[2:].split(":")
assert i + 1 == int(number)
identifiers.append(identifier.strip())
if len(identifiers) == number_of_sequences:
break
elif key == "Matrix":
annotations[key] = value.strip()
elif key == "Gap_penalty":
annotations[key] = float(value.strip())
elif key == "Extend_penalty":
annotations[key] = float(value.strip())
elif key == "Length":
ncols = int(value.strip())
elif key == "Identity":
annotations[key] = int(value.strip().split("/")[0])
elif key == "Similarity":
annotations[key] = int(value.strip().split("/")[0])
elif key == "Gaps":
annotations[key] = int(value.strip().split("/")[0])
elif key == "Score":
annotations[key] = float(value.strip())
# TODO:
# The following are generated if the -nobrief command line
# argument used. We could simply calculate them from the
# alignment, but then we have to define what we mean by
# "similar". For now, simply store them as an annotation.
elif key == "Longest_Identity":
annotations[key] = value.strip()
elif key == "Longest_Similarity":
annotations[key] = value.strip()
elif key == "Shortest_Identity":
annotations[key] = value.strip()
elif key == "Shortest_Similarity":
annotations[key] = value.strip()
else:
raise ValueError("Failed to parse line '%s'" % line)
else:
return
if len(identifiers) == 0:
raise ValueError("Number of sequences missing!")
if ncols is None:
raise ValueError("Length of alignment missing!")
sequences = [""] * number_of_sequences
aligned_sequences = [""] * number_of_sequences
consensus = ""
starts = [0] * number_of_sequences
ends = [0] * number_of_sequences
column = 0
index = 0
for line in stream:
line = line.rstrip("\r\n")
# parse the sequences
if not line:
# empty line
if index == number_of_sequences:
# reached the end of an alignment block
if column == ncols:
# reached the end of the sequences
break
index = 0
continue
prefix = line[:21].strip()
if prefix == "":
# match line
consensus += line[21:71]
else:
identifier, start = prefix.split(None, 1)
assert identifiers[index].startswith(identifier)
aligned_sequence, end = line[21:].split(None, 1)
start = int(start)
end = int(end)
length = len(sequences[index])
sequence = aligned_sequence.replace("-", "")
if length == 0 and len(sequence) > 0:
if start < end:
start -= 1 # Python counting
assert end == start + len(sequence)
else:
end -= 1 # Python counting
assert end == start - len(sequence)
# Record the start
starts[index] = start
else:
if starts[index] <= ends[index]:
# forward strand
if (
self.metadata["Align_format"] == "srspair"
and len(sequence) == 0
):
assert start == ends[index]
assert end == start
else:
start -= 1
assert end == start + len(sequence)
else:
if (
self.metadata["Align_format"] == "srspair"
and len(sequence) == 0
):
assert start - 1 == ends[index]
assert end == start
else:
end -= 1
assert end == start - len(sequence)
# Record the end
ends[index] = end
sequences[index] += sequence
aligned_sequences[index] += aligned_sequence
if index == 0:
column += len(aligned_sequence)
else:
assert column == len(aligned_sequences[index])
index += 1
aligned_sequences = [
aligned_sequence.encode() for aligned_sequence in aligned_sequences
]
sequences, coordinates = Alignment.parse_printed_alignment(aligned_sequences)
records = []
n = len(sequences)
for i in range(n):
start = starts[i]
end = ends[i]
data = sequences[i]
if start == 0:
sequence = Seq(data)
elif start < end:
coordinates[i, :] += start
# create a partially defined sequence
sequence = Seq({start: data}, length=end)
else:
start, end = end, start
coordinates[i, :] = end - coordinates[i, :]
# create a partially defined sequence
sequence = Seq({0: data}, length=end).reverse_complement()
record = SeqRecord(sequence, identifiers[i])
records.append(record)
alignment = Alignment(records, coordinates)
if annotations:
alignment.annotations = annotations
if consensus:
alignment.column_annotations = {"emboss_consensus": consensus}
return alignment
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