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#!/usr/bin/env python
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""
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):
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):
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):
"""
>>> 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):
"""
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()
main()
|
