[Bioperl-l] possible filehandle out of scope bug between
Bio::AlignIO and Bio::Tools::Run::Hmmer  Scott Markel smarkel at
scitegic.com Mon Apr 18 15:17:10 EDT 2005  Note: The context for
this message assumes the code change to Bio::Tools::Run::Hmmer
that I just sent to the mailing  I'm running BioPerl-1.4 on both
Windows XP (Perl 5.8.0) and cygwin (Perl 5.8.5).  I get the same
behavior when I use  When I run the following code, I get the
error message     Can't call method "consensus_string" on an
undefined value    at runHmmAlign.pl line 14.  If I change
$factory to $::factory, so that it doesn't go out of scope when
the subroutine is done, then everything is fine.  My Perl
debugging skills aren't what they should be, so I'm not sure how
to verify the following, but it looks like the destructor for
Bio::Tools::Run::Hmmer clobbers the filehandle in Bio::AlignIO.
Similar code involving Bio::Tools::Run::Hmmer and Bio::SearchIO
(for hmmsearch) does not have this problem.  I checked the bug
list, but didn't find