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

source code

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'