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

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:

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

Classes [hide private]
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]
  _CMDLINE_DNAL = ['dnal', '-alb', '-nopretty']
  _CMDLINE_FGREP_COUNT = 'fgrep -c \'%s\' %s'
  _re_alb_line2coords = re.compile(r'^\[([^:]+):[^\[]+\[([^:]+):')
  __package__ = 'Bio.Wise'