/usr/share/pyshared/Bio/Wise/psw.py is in python-biopython 1.58-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 | #!/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
__version__ = "$Revision: 1.5 $"
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, sys
doctest.testmod(sys.modules[__name__], *args, **keywds)
if __name__ == "__main__":
if __debug__:
_test()
main()
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