Re: [Boost-users] follow up on regex questions(one more observation)

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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