Module dnal

Version: $Revision: 1.12 $

Classes

Statistics
Calculate statistics from an ALB report

Functions

_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

_any(seq, pred=<type 'bool'>)
Returns True if pred(x) is True at least one element in the iterable

source code

align(pair, match=4, mismatch=-1, gap=-5, extension=-1, **keywds)

source code

main()

source code

_test(*args, **keywds)

source code

Variables

_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'