[Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Apr 21 17:00:32 EDT 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2476





------- Comment #4 from cjfields at uiuc.edu  2008-04-21 17:00 EST -------
This has mainly been fixed in bioperl-live.  There are a few warnings which
still appear (and differ from the previous ones):

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Undefined sub-sequence (600,600). Valid range = 600 - 644
STACK: Error::throw
STACK: Bio::Root::Root::throw
/Users/cjfields/bioperl/bioperl-live/Bio/Root/Root.pm:357
STACK: Bio::Search::HSP::HSPI::matches
/Users/cjfields/bioperl/bioperl-live/Bio/Search/HSP/HSPI.pm:691
STACK: Bio::Search::SearchUtils::_adjust_contigs
/Users/cjfields/bioperl/bioperl-live/Bio/Search/SearchUtils.pm:460
STACK: Bio::Search::SearchUtils::tile_hsps
/Users/cjfields/bioperl/bioperl-live/Bio/Search/SearchUtils.pm:206
STACK: test_tblastx.pl:14
-----------------------------------------------------------

I'll leave this open for now but can't promise when this'll be fixed (most of
the core devs have been very busy as of late).  This code is notoriously
'brittle' (as Jason puts it) and several suggestions in the past have indicated
this may need some refactoring.  Maybe for the next bioperl-dev?


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