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#!/usr/bin/env python
# Copyright 2004 by Michael Hoffman. 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.
"""Run and process output from the Wise2 package tool psw.
Bio.Wise contains modules for running and processing the output of
some of the models in the Wise2 package by Ewan Birney available from:
ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/
http://www.ebi.ac.uk/Wise2/
Bio.Wise.psw is for protein Smith-Waterman alignments
Bio.Wise.dnal is for Smith-Waterman DNA alignments
"""
from __future__ import print_function
import os
import re
import sys
from Bio import Wise
_CMDLINE_PSW = ["psw", "-l", "-F"]
_OPTION_GAP_START = "-g"
_OPTION_GAP_EXTENSION = "-e"
_OPTION_SCORES = "-m"
class AlignmentColumnFullException(Exception):
pass
class Alignment(list):
def append(self, column_unit):
try:
self[-1].append(column_unit)
except AlignmentColumnFullException:
list.append(self, AlignmentColumn(column_unit))
except IndexError:
list.append(self, AlignmentColumn(column_unit))
class AlignmentColumn(list):
def _set_kind(self, column_unit):
if self.kind == "SEQUENCE":
self.kind = column_unit.kind
def __init__(self, column_unit):
"""Initialize the class."""
assert column_unit.unit == 0
self.kind = column_unit.kind
list.__init__(self, [column_unit.column, None])
def __repr__(self):
return "%s(%s, %s)" % (self.kind, self[0], self[1])
def append(self, column_unit):
if self[1] is not None:
raise AlignmentColumnFullException
assert column_unit.unit == 1
self._set_kind(column_unit)
self[1] = column_unit.column
class ColumnUnit(object):
def __init__(self, unit, column, kind):
"""Initialize the class."""
self.unit = unit
self.column = column
self.kind = kind
def __str__(self):
return "ColumnUnit(unit=%s, column=%s, %s)" % (self.unit, self.column, self.kind)
__repr__ = __str__
_re_unit = re.compile(r"^Unit +([01])- \[ *(-?\d+)- *(-?\d+)\] \[(\w+)\]$")
def parse_line(line):
"""Parse a line from psw.
>>> print(parse_line("Column 0:"))
None
>>> parse_line("Unit 0- [ -1- 0] [SEQUENCE]")
ColumnUnit(unit=0, column=0, SEQUENCE)
>>> parse_line("Unit 1- [ 85- 86] [SEQUENCE]")
ColumnUnit(unit=1, column=86, SEQUENCE)
"""
match = _re_unit.match(line.rstrip())
if not match:
return
return ColumnUnit(int(match.group(1)), int(match.group(3)), match.group(4))
def parse(iterable):
"""Parse a file.
format
Column 0:
Unit 0- [ -1- 0] [SEQUENCE]
Unit 1- [ 85- 86] [SEQUENCE]
means that seq1[0] == seq2[86] (0-based)
"""
alignment = Alignment()
for line in iterable:
try:
if os.environ["WISE_PY_DEBUG"]:
print(line)
except KeyError:
pass
column_unit = parse_line(line)
if column_unit:
alignment.append(column_unit)
return alignment
def align(pair,
scores=None,
gap_start=None,
gap_extension=None,
*args, **keywds):
cmdline = _CMDLINE_PSW[:]
if scores:
cmdline.extend((_OPTION_SCORES, scores))
if gap_start:
cmdline.extend((_OPTION_GAP_START, str(gap_start)))
if gap_extension:
cmdline.extend((_OPTION_GAP_EXTENSION, str(gap_extension)))
temp_file = Wise.align(cmdline, pair, *args, **keywds)
return parse(temp_file)
def main():
print(align(sys.argv[1:3]))
def _test(*args, **keywds):
import doctest
doctest.testmod(sys.modules[__name__], *args, **keywds)
if __name__ == "__main__":
if __debug__:
_test()
"""Initialize the class."""
main()
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