[Gmod-help] Re: [Gmod-gbrowse] UCSC Plug-in Conservation tracks won't display

[Bill Pulec]

Hi Dave and all,
    I have actually (semi-)resolved the issue. First I should have noted
that I added an extra line of code so when I get the error on line 440, that
actually refers to line 439 of UcscConservation.pm.

It seems the issue is that the trackDB table in the database I was using did
not have entries for all the conservation tracks. I simple switched to an
alignment that had the proper entry in the trackDB table.

-Bill

On Thu, May 14, 2009 at 4:41 PM, Dave Clements, GMOD Help Desk <
gmodhelp at googlemail.com> wrote:

> Hi Bill,
>
> The error you are seeing is actually a warning, and is often ignorable
> in Perl programs.  However, I don't think that is the case here.  Line
> 440 of the latest UcscConservation.pm is:
>
>   412  sub annotate {
>   413    my $self = shift;
>   414    my $segment = shift;
>   415    my $config  = $self->configuration;
>   416    $self->get_browser_config_settings() unless $self->{db};
>   417    return unless defined %$config;
>   418
>   419    warn("UcscConservation annotate start " . `date`) if DEBUG;
>   420
>   421    my $ref        = $segment->seq_id;
>   422    my $abs_start  = $segment->start;
>   423    my $abs_end    = $segment->end;
>   424
>   425    my $feature_list = $self->new_feature_list;
>   426
>   427    my @wigMafTracks = grep {($config->{$_} && s/^enable_// &&
>   428                              $self->table_exists($_, $ref))}
> keys %$config;
>   429    if (scalar(@wigMafTracks) == 0) {
>   430      if ($self->{default_enable}) {
>   431        @wigMafTracks = grep {s/^enable_// &&
> $self->table_exists($_, $ref)}
>   432          keys %{$self->{default_enable}};
>   433      } elsif ($config->{'enableAll'}) {
>   434        @wigMafTracks = $self->list_tracks_by_type('wigMaf');
>   435      }
>   436    }
>   437    @wigMafTracks = $self->sort_by_trackDb_priority(@wigMafTracks);
>   438    foreach my $track (@wigMafTracks) {
>   439      my $label = $self->get_trackDb_val($track, 'longLabel') . '
> (UCSC)';
>   440      $feature_list->add_type($track=>{glyph   => 'ucsc_glyph',
>   441                                       key     => $label,
>   442                                      });
>   443      my $feature = $self->wigMaf_feature($track, $ref,
> $abs_start, $abs_end);
>   444      $feature_list->add_feature($feature, $track);
>   445    }
>   446    warn("UcscConservation annotate end   " . `date`) if DEBUG;
>   447    return $feature_list;
>   448  }
>
> According to my limited Perl understanding, I think all variables in
> line 440 should be defined, so I have no idea what is going on here.
>
> Does anyone else have any insight into what Bill is seeing?  Could
> this error even be causing what he is seeing?
>
> Thanks,
>
> Dave C.
>
> On Tue, May 12, 2009 at 9:17 AM, Bill Pulec <wpulec at gmail.com> wrote:
> > Hi All,-
> >   I have some conservation tracks that I have been trying to add to a
> > database using the UCSC plug-in, but I always get an error when I try to
> > open the tracks in Gbrowse. I know that the UCSC plug-in,
> > UcscTrackImage.conf and the hgcentral database must be working because I
> > have set up conservation tracks for other databases, and they work fine.
> > When grbrowse loads the failing conservation tracks all the tracks and
> the
> > settings below the tracks do not load.
> >
> > There is an error in the error log:
> >
> > Use of uninitialized value in concatenation (.) or string at
> > /etc/httpd/conf/gbrowse.conf/plugins/UcscConservation.pm line 440.,
> referer:
> > <NameOfMyServer>
> >
> > This seems to me like UcscConservation.pm can't find the correct file on
> my
> > hard drive that the MySQL tables refer to, but the file seems to be in
> the
> > correct location with the correct file name. So I am not sure why it
> cannot
> > find the file.
> >
> > If anyone has any insights into what is going on it would be greatly
> > appreciated.
> >
> > Thanks,
> > Bill
> >
> >
> >
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