[Bioperl-l] Problems with Unflattener.pm

[Chris Fields]

I was able to reproduce this using WinXP and bioperl-live.  Seems to get
caught up in the loop during recursion: debugging shows it is unable to get
past 'find_best_matches: (/15)'.  There are lots of unmatched pairs here
with this sequence, so could that be the problem?  I not terribly familiar
with Unflattener...

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Barry Moore
> Sent: Monday, May 22, 2006 8:00 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] Problems with Unflattener.pm
> 
> Hi All,
> 
> NT_113910 appears to throw Bio::SeqFeatures::Tools::Unflattener into
> an infinite recursive loop.  The trouble occurs in the method
> find_best_matches between lines 2258 and 2281, and in particular the
> loop is perpetuated by line 2273.   NT_113910 has a fairly complex
> features table, and but I have as yet been unable to figure out why
> this loop is not exiting properly.  This has been submitted to
> bugzilla, but I'll post here so it gets documented on the list also.
> Any suggestions from Chris or others would be greatly appreciated.
> 
> This problem can be recreated as follows:
> 
> Grab NT_113910 from genbank.
> bp_fetch.pl -fmt genbank net::genbank:NT_113910 > NT_113910.gbk
> 
> Pass NT_113910.gbk on the command line to the attached script.
> 
> 
> 
> #!/usr/bin/perl;
> 
> use strict;
> use warnings;
> 
> use Bio::SeqIO;
> use Bio::SeqFeature::Tools::Unflattener;
> 
> my $file = shift;
> 
> # generate an Unflattener object
> my $unflattener = Bio::SeqFeature::Tools::Unflattener->new;
> #$unflattener->verbose(1);
> 
> # first fetch a genbank SeqI object
> my $seqio =
>      Bio::SeqIO->new(-file   => $file,
>                      -format => 'GenBank');
> my $out =
>      Bio::SeqIO->new(-format => 'asciitree');
> while (my $seq = $seqio->next_seq()) {
> 
>          # get top level unflattended SeqFeatureI objects
>          $unflattener->unflatten_seq(-seq       => $seq,
>                                      -use_magic => 1);
>          $out->write_seq($seq);
> }
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l