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# 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 A2M files.

A2M files are alignment files created by align2model or hmmscore in the SAM

Sequence Alignment and Modeling Software System.

"""

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 A2M file format."""

fmt = "A2M"

def format_alignment(self, alignment):

"""Return a string with the alignment in the A2M file format."""

if not isinstance(alignment, Alignment):

raise TypeError("Expected an Alignment object")

lines = []

state = alignment.column_annotations["state"]

for sequence, line in zip(alignment.sequences, alignment):

try:

name = sequence.id

except AttributeError:

name = ""

try:

description = sequence.description

except AttributeError:

description = ""

if description:

lines.append(f">{name} {description}")

else:

lines.append(f">{name}")

s = ""

for c, m in zip(line, state):

if m == "D":

s += c.upper()

elif m == "I":

if c == "-":

s += "."

else:

s += c.lower()

lines.append(s)

return "\n".join(lines) + "\n"

write_alignments = interfaces.AlignmentWriter.write_single_alignment

class AlignmentIterator(interfaces.AlignmentIterator):

"""Alignment iterator for files in the A2M file format.

An A2M file contains one multiple alignment. Matches are represented by

upper case letters and deletions by dashes in alignment columns containing

matches or deletions only. Insertions are represented by lower case letters,

with gaps aligned to the insertion shown as periods. Header lines start

with '>' followed by the name of the sequence, and optionally a description.

"""

fmt = "A2M"

def _read_next_alignment(self, stream):

names = []

descriptions = []

lines = []

for line in stream:

if line.startswith(">"):

parts = line[1:].rstrip().split(None, 1)

try:

name = parts[0]

except IndexError:

name = ""

try:

description = parts[1]

except IndexError:

description = ""

names.append(name)

descriptions.append(description)

lines.append("")

else:

lines[-1] += line.strip()

if not lines:

if self._stream.tell() == 0:

raise ValueError("Empty file.")

return

state = ""

for c in lines[0]:

if c == "-" or c.isupper():

state += "D" # Match/deletion state

elif c == "." or c.islower():

state += "I" # Insertion state

else:

raise Exception("Unexpected letter '%s' in alignment" % c)

for line in lines[1:]:

for c, m in zip(line, state):

if m == "D": # Match/deletion state

assert c == "-" or c.isupper()

elif m == "I": # Insertion state

assert c == "." or c.islower()

else:

raise Exception("Unexpected letter '%s' in alignment" % c)

for i, line in enumerate(lines):

lines[i] = line.upper().replace(".", "-").encode()

seqdata, coordinates = Alignment.parse_printed_alignment(lines)

records = []

for name, description, seqrow in zip(names, descriptions, seqdata):

sequence = Seq(seqrow)

record = SeqRecord(sequence, name, description=description)

records.append(record)

alignment = Alignment(records, coordinates)

alignment.column_annotations = {}

alignment.column_annotations["state"] = state

return alignment

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