[Bioperl-l] questions about generating gene model by GLEAN

[Aaron Mackey]

Hi Shuai,

As I wrote yesterday, please send me your .yaml file, as there is probably
something in there causing the problem.

-Aaron

--
Aaron J. Mackey, PhD
Assistant Professor
Center for Public Health Genomics
University of Virginia
amackey at virginia.edu
http://www.cphg.virginia.edu/mackey


On Fri, Jan 28, 2011 at 1:03 PM, Zhan, Shuai <Shuai.Zhan at umassmed.edu>wrote:

> Hi,
>
> Is there someone used GLEAN for generating consensus gene set? Would you
> mind sharing some experience with me? I'd greatly appreciate any help.
>
> I have tried for run it for couple of weeks. At first I found it can't
> fetch the real sequence from database but on object, then I change some some
> codes of fetchseq {} of GLEAN::Evidence::Base. (->seq->seq instead of ->seq)
>
> By far, it has began processing my input and correctly analyzed the
> candidate start, stop, donor, and acceptor for the first contig.
> But it still failed with something looks like "MSG: asking for tag value
> that does not exist Evidence".
>
> $glean-lca --database glean --user me --password 123  --param param.yaml >
> test.dat
> No reference provided; attempting to analyze entire genome
> Gathering evidence from 'FGENE' for scaff Contig0:1,1129007 ...
> The initial exon of CDS:FGENESH(fgp17144.t1) did not begin with a valid
> start codon
> Extending the terminal exon of CDS:FGENESH(fgp17240.t1) to next valid
> downstream stop codon
> The initial exon of CDS:FGENESH(fgp17165.t1) did not begin with a valid
> start codon
> Extending the initial exon of CDS:FGENESH(fgp17192.t1) to next valid
> upstream start codon
> The initial exon of CDS:FGENESH(fgp17178.t1) did not begin with a valid
> start codon
> Error providing evidence type: GeneModel
> The error was:
> ------------- EXCEPTION -------------
> MSG: asking for tag value that does not exist Evidence
> STACK Bio::SeqFeature::Generic::get_tag_values
> /usr/lib/perl5/site_perl/5.8.8/Bio/SeqFeature/Generic.pm:517
> STACK Glean::Site::dump
> /home/zhan/geneset/glean-gene/bin/../lib/Glean/Site.pm:52
> STACK Glean::MLE::_add_evidence
> /home/zhan/geneset/glean-gene/bin/../lib/Glean/MLE.pm:167
> STACK Glean::MLE::add_evidence
> /home/zhan/geneset/glean-gene/bin/../lib/Glean/MLE.pm:94
> STACK (eval) /home/zhan/geneset/glean-gene/bin/../lib/Glean/MLE.pm:203
> STACK Glean::MLE::estimate
> /home/zhan/geneset/glean-gene/bin/../lib/Glean/MLE.pm:202
> STACK toplevel glean-gene/bin/glean-lca:172
>
> I think it failed in add_evidence method of Glean::MLE.
> According to the track, I also report some key scalar by print sentense.
>
> For example,
> It failed in adding the first candidate site to evidence.
> The current $site is Contig0:1011027:1011027:0:-1, its primary_tag is
> "start", its seq_id is "Contig0" its strand is -1.
> At first it invoked _add_evidence {} of Glean/MLE.pm.
> The problem is $site->dump need get the value of tag "Evidence" for $site,
> but actually the "Evidence" tag didn't exist for this site.
> THen I found $site of @sites was created by list_starts {} of
> Glean::Evidence::GeneModel, but its inital tags only have "Next Stop" and
> "Readingframe". I can't find any hint of when tag "Evidence" was added to
> $site.
>
> The related source codes of glean are listed:
> sub _add_evidence{
>  my @sites = $evid->list_sites($scaff);
>  for my $site (@sites) {
>    ...
>    $stype->{$sloc}->{_site} ||= $site->dump;
>  }
>  ...
> }
> sub dump { # from Glean/Site.pm
>  ...
>  return join("\t",
>              $site->seq_id,
>              $site->primary_tag,
>              defined $site->score ? sprintf("%g", $site->score == 0 ?
> $site->worst : -log($site->score)) : "NA",
>              ...
>              join(";", $site->get_tag_values("Evidence"))
>             );
>  ...
> }
> sub list_sites { # from Evidence/GeneModel.pm
>  ...
>  push @sites, $self->list_starts(@cds);
>  ...
> }
> sub list_starts { # from Evidence/GeneModel.pm
>  ...
>  push @sites, Glean::Site->new(-primary => "start",
>                                  -start   => $pos + $str * (pos($startseq)
> - 3),
>                                  -end     => $pos + $str * (pos($startseq)
> - 3),
>                                  -strand  => $str,
>                                  -frame   => 0,
>                                  -source  => "$self",
>                                  -seq_id  => $seq_id,
>                                  -tag => { NextStop => $nextstop,
>                                            ReadingFrame => $frame,
>                                          },
>                                 );
>  ...
> }
> sub add_evidence{
>  ...
>  eval {
>    $self->add_evidence($scaff, $evtype->new($db, $self->{_log}, $algo,
> $params));
>  };
>  croak("Error providing evidence type: $type\nThe error was:\n$@") if $@;
>  ...
> }
>
> Sincerely
> Shuai Zhan
>
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