Bio.Wise.dnal module

Run and process output from the Wise2 package tool dnal.

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

class Bio.Wise.dnal.Statistics(filename, match, mismatch, gap, extension)

Bases: object

Calculate statistics from an ALB report.

__init__(filename, match, mismatch, gap, extension)

Initialize the class.

identity_fraction()

Calculate the fraction of matches.

header = 'identity_fraction\tmatches\tmismatches\tgaps\textensions'

__str__()

Statistics as a tab separated string.

Bio.Wise.dnal.align(pair, match=_SCORE_MATCH, mismatch=_SCORE_MISMATCH, gap=_SCORE_GAP_START, extension=_SCORE_GAP_EXTENSION, **keywds)

Align a pair of DNA files using dnal and calculate the statistics of the alignment.

Bio.Wise.dnal.main()

Command line implementation.