Package Bio :: Package Wise :: Module psw
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Module Bio.Wise.psw

Classes
Alignment  
AlignmentColumn  
ColumnUnit  

Exceptions
AlignmentColumnFullException  

Function Summary
  align(pair, scores, gap_start, gap_extension, *args, **keywds)
  main()
  parse(iterable)
format
  parse_line(line)
  _test(*args, **keywds)

Variable Summary
str __version__ = '$Revision: 1.3 $'
list _CMDLINE_PSW = ['psw', '-l', '-F']
str _OPTION_GAP_EXTENSION = '-e'
str _OPTION_GAP_START = '-g'
str _OPTION_SCORES = '-m'
SRE_Pattern _re_unit = ^Unit +([01])\[ *(-?\d+)*(-?\d+)\] \[(\w+...

Function Details

parse(iterable)

format

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

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

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)

Variable Details

__version__

Type:
str
Value:
'$Revision: 1.3 $'                                                     

_CMDLINE_PSW

Type:
list
Value:
['psw', '-l', '-F']                                                    

_OPTION_GAP_EXTENSION

Type:
str
Value:
'-e'                                                                   

_OPTION_GAP_START

Type:
str
Value:
'-g'                                                                   

_OPTION_SCORES

Type:
str
Value:
'-m'                                                                   

_re_unit

Type:
SRE_Pattern
Value:
^Unit +([01])- \[ *(-?\d+)- *(-?\d+)\] \[(\w+)\]$                      

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