Package Bio :: Package Wise :: Module psw

[frames] | no frames]

Module psw

Version: $Revision: 1.5 $

Classes

AlignmentColumnFullException

Alignment

AlignmentColumn

ColumnUnit

Functions

parse_line(line)
>>> print parse_line("Column 0:")...

source code

parse(iterable)
format

source code

align(pair, scores=None, gap_start=None, gap_extension=None, *args, **keywds)

source code

main()

source code

_test(*args, **keywds)

source code

Variables

_CMDLINE_PSW = ['psw', '-l', '-F']

_OPTION_GAP_START = '-g'

_OPTION_GAP_EXTENSION = '-e'

_OPTION_SCORES = '-m'

_re_unit = re.compile(r'^Unit +([01])- \[ *(-?\d+)- *(-?\d+)\]...

Function Details

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)

parse(iterable)


format

Column 0:
Unit  0- [  -1-   0] [SEQUENCE]
Unit  1- [  85-  86] [SEQUENCE]

means that seq1[0] == seq2[86] (0-based)

Variables Details

_re_unit

Value:

re.compile(r'^Unit +([01])- \[ *(-?\d+)- *(-?\d+)\] \[(\w+)\]$')