Package Bio :: Package Wise :: Module dnal
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Module dnal

source code

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

Classes [hide private]
  Statistics
Calculate statistics from an ALB report.
Functions [hide private]
 
_build_dnal_cmdline(match, mismatch, gap, extension) source code
 
_fgrep_count(pattern, file) source code
 
_alb_line2coords(line) source code
 
_get_coords(filename) source code
 
align(pair, match=4, mismatch=-1, gap=-5, extension=-1, **keywds) source code
 
main() source code
 
_test(*args, **keywds) source code
Variables [hide private]
  _SCORE_MATCH = 4
  _SCORE_MISMATCH = -1
  _SCORE_GAP_START = -5
  _SCORE_GAP_EXTENSION = -1
  _CMDLINE_DNAL = ['dnal', '-alb', '-nopretty']
  _CMDLINE_FGREP_COUNT = 'fgrep -c \'%s\' %s'
  _re_alb_line2coords = re.compile(r'^\[([^:]+):[^\[]+\[([^:]+):')
  __package__ = 'Bio.Wise'