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Package Bio :: Package Wise :: Module dnal |
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Classes | |
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Statistics |
Calculate statistics from an ALB report |
Function Summary | |
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align(pair,
match,
mismatch,
gap,
extension,
**keywds)
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main()
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_alb_line2coords(line)
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Returns True if pred(x) is True at least one element in the iterable | |
_build_dnal_cmdline(match,
mismatch,
gap,
extension)
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_fgrep_count(pattern,
file)
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_get_coords(filename)
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_test(*args,
**keywds)
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Variable Summary | |
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str |
__version__ = '$Revision: 1.9 $'
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list |
_CMDLINE_DNAL = ['dnal', '-alb', '-nopretty']
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str |
_CMDLINE_FGREP_COUNT = "fgrep -c '%s' %s"
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SRE_Pattern |
_re_alb_line2coords = ^\[([^:]+):[^\[]+\[([^:]+):
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int |
_SCORE_GAP_EXTENSION = -1 |
int |
_SCORE_GAP_START = -5 |
int |
_SCORE_MATCH = 4 |
int |
_SCORE_MISMATCH = -1 |
Function Details |
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_any(seq, pred=<type 'bool'>)Returns True if pred(x) is True at least one element in the iterable |
Variable Details |
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__version__
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_CMDLINE_DNAL
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_CMDLINE_FGREP_COUNT
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_re_alb_line2coords
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_SCORE_GAP_EXTENSION
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_SCORE_GAP_START
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_SCORE_MATCH
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_SCORE_MISMATCH
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