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

source code

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) 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 [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 

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])- \[ *(-?\d+)- *(-?\d+)\] \[(\w+)\]$')