Bio.Wise.dnal

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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