Bio.Wise package

Module contents

Run and process output from the Wise2 package tools.

Bio.Wise contains modules for running and processing the output of some of the models in the Wise2 package by Ewan Birney available from:

Bio.Wise.psw is for protein Smith-Waterman alignments Bio.Wise.dnal is for Smith-Waterman DNA alignments

Bio.Wise.align(cmdline, pair, kbyte=None, force_type=None, dry_run=False, quiet=False, debug=False)

Run an alignment. Returns a filehandle.


Generate pairs list for all-against-all alignments.

>>> all_pairs(range(4))
[(0, 1), (0, 2), (0, 3), (1, 2), (1, 3), (2, 3)]

Provision for command line testing.