From: Mike Marchywka (marchywka_at_[hidden])
Date: 2007-10-04 17:48:26
Thanks again for responding- I know how annoying these problems are where
there are so many posisble issues. But, let me review what does appear
to work. I have a list of 1300 regex "rules." I can verify that I get the
same results
with greta and boost in my annotation program using commands like this:
( rules_annotater is my test program that applies -xrules to -fastas input
file
and reports results on stdout):
319 $progpath/rules_annotater -boost -doall -fastas onn_fastas -xrules
$progpath/prosite_rules > xxxx
321 $progpath/rules_annotater -clean -doall -fastas onn_fastas -xrules
$progpath/prosite_rules > yyyy
322 diff xxxx yyyy
The diff is clean. I have 1320 rules and the input file contains about 30
text samples,
$ more $progpath/prosite_rules | wc
1319 5276 116804
and I get about 2231 hits from the above input data ( "onn_fastas" contains
several input strings)
$ more xxxx | wc
2231 13406 125169
However, there are very few groups, in fact,
( boost only sees the first word as none of these have white space)
$ more $progpath/prosite_rules | grep "("
F[GSTV]PRL([G]|$) >rule|1074|PEPDTIDE Prosite PYROKININ
F[IVFY]G[LM]M([G]|$) >rule|1077|PEPDTIDE Prosite TACHYKININ
That is why I hope to figure out why the other rule set, containing only 3
rules,
has consistent problems. If I thought the build was just plain bad I'd stop
everything
and fix that first but the only apparent problem is an inability to throw
from boost.
While I had been testing with different program options, I did just verify
that
the slight modification to the above command,
$ $progpath/rules_annotater -boost -doall -fastas onn_fastas -xrules
$progpa
th/boost_edit_rulesx
will hang when the edit rules file contains things like this:
.(...)*?(.)?(H|F|G) >rule|4|Test test
Thanks again.
Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165
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marchywka_at_[hidden]
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me on marchywka_at_[hidden] if no reply
here. Thanks.
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