Package Bio :: Package Wise
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Package Wise

source code

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: 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

Submodules [hide private]
  • Bio.Wise.dnal: Run and process output from the Wise2 package tool dnal.
  • Bio.Wise.psw: Run and process output from the Wise2 package tool psw.

Functions [hide private]
 
_build_align_cmdline(cmdline, pair, output_filename, kbyte=None, force_type=None, quiet=False)
Helper function to build a command line string (PRIVATE).
source code
 
align(cmdline, pair, kbyte=None, force_type=None, dry_run=False, quiet=False, debug=False)
Run an alignment. Returns a filehandle.
source code
 
all_pairs(singles)
Generate pairs list for all-against-all alignments.
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main() source code
 
_test(*args, **keywds) source code
Variables [hide private]
  __package__ = 'Bio.Wise'