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

source code

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

Classes [hide private]
  AlignmentColumnFullException
  Alignment
  AlignmentColumn
  ColumnUnit
Functions [hide private]
 
parse_line(line)
Parse a line from psw.
source code
 
parse(iterable)
Parse a file.
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 [hide private]
  _CMDLINE_PSW = ['psw', '-l', '-F']
  _OPTION_GAP_START = '-g'
  _OPTION_GAP_EXTENSION = '-e'
  _OPTION_SCORES = '-m'
  _re_unit = re.compile(r'^Unit +([01])- \[ *(-?\d+)- *(-?\d+)\]...
  __package__ = 'Bio.Wise'
Function Details [hide private]

parse(iterable)

source code 

Parse a file.

format

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

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


Variables Details [hide private]

_re_unit

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