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

Classes
Statistics Calculate statistics from an ALB report

Function Summary
  align(pair, match, mismatch, gap, extension, **keywds)
  main()
  _alb_line2coords(line)
  _any(seq, pred)
Returns True if pred(x) is True at least one element in the iterable
  _build_dnal_cmdline(match, mismatch, gap, extension)
  _fgrep_count(pattern, file)
  _get_coords(filename)
  _test(*args, **keywds)

Variable Summary
str __version__ = '$Revision: 1.9 $'
list _CMDLINE_DNAL = ['dnal', '-alb', '-nopretty']
str _CMDLINE_FGREP_COUNT = "fgrep -c '%s' %s"
SRE_Pattern _re_alb_line2coords = ^\[([^:]+):[^\[]+\[([^:]+):
int _SCORE_GAP_EXTENSION = -1                                                                    
int _SCORE_GAP_START = -5                                                                    
int _SCORE_MATCH = 4                                                                     
int _SCORE_MISMATCH = -1                                                                    

Function Details

_any(seq, pred=<type 'bool'>)

Returns True if pred(x) is True at least one element in the iterable

Variable Details

__version__

Type:
str
Value:
'$Revision: 1.9 $'                                                     

_CMDLINE_DNAL

Type:
list
Value:
['dnal', '-alb', '-nopretty']                                          

_CMDLINE_FGREP_COUNT

Type:
str
Value:
"fgrep -c '%s' %s"                                                     

_re_alb_line2coords

Type:
SRE_Pattern
Value:
^\[([^:]+):[^\[]+\[([^:]+):                                            

_SCORE_GAP_EXTENSION

Type:
int
Value:
-1                                                                    

_SCORE_GAP_START

Type:
int
Value:
-5                                                                    

_SCORE_MATCH

Type:
int
Value:
4                                                                     

_SCORE_MISMATCH

Type:
int
Value:
-1                                                                    

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