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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
404-788-1216 (C)<- leave message
989-348-4796 (P)<- emergency only
marchywka_at_[hidden]
Note: Hotmail is blocking my mom's entire
ISP claiming it is to reduce spam but probably
to force users to use hotmail. Please DON'T
assume I am ignoring you and try
me on marchywka_at_[hidden] if no reply
here. Thanks.

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