[Gmod-help] Re: [Gmod-gbrowse] Error messages when viewing gbrowse_details

[Wes Barris]

Dave Clements, GMOD Help Desk wrote:
> Hi Wes,
> 
> To the best of my knowledge there is no switch to say "I don't have
> sequence."  FASTA has either been loaded, or it hasn't.
> 
> This might be a bug.
> 
> Dave C

I've tracked down the error message to the last line of this
routine inside gbrowse_details:

sub get_seq {
     my $self = shift;
     my $f     = shift;
     my $ref   = $f->seq_id;
     my $start = $f->start;
     my $end   = $f->end;
     my $strand = $f->strand;

     # the sequence must live in the database flagged in the [GENERAL] section
     my $db    = $self->source->open_database() or return;
     my ($seg) = $db->segment($ref,$start,$end) or return;
     return $strand >= 0 ? $seg->seq : $seg->seq->revcom;
}

If I insert a "return '';" just before the last line I can prevent
the errors from appearing.  When I print out the value of $seg I
get a string like this: "BTA14:24975789..24977098".

I don't know enough about how this is supposed to work to do any
more.  $seg appears to be just a string not an object.

> On Mon, Feb 1, 2010 at 5:34 PM, Wes Barris <wes.barris at csiro.au> wrote:
>> When I view the gbrowse_details page for a feature I get a boatload
>> of errors in the web error log file.  The errors indicate that it
>> assumes I have sequence data loaded.  Is there a configuration
>> setting that I can use to tell gbrowse that I do not have sequence
>> data loaded?  This is for gbrowse2.  Here are the first few lines
>> of errors:
>>
>> [Tue Feb 02 11:30:13 2010] [error] [client 140.253.153.217]
>> [Tue Feb 02 11:30:13 2010] [error] [client 140.253.153.217] --------------------- WARNING ---------------------
>> [Tue Feb 02 11:30:13 2010] [error] [client 140.253.153.217] MSG: Got a sequence with no letters in it cannot guess alphabet
>> [Tue Feb 02 11:30:13 2010] [error] [client 140.253.153.217] ---------------------------------------------------
>> [Tue Feb 02 11:30:13 2010] [error] [client 140.253.153.217] Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/5.8.5/Bio/PrimarySeqI.pm line 368.
>> [Tue Feb 02 11:30:13 2010] [error] [client 140.253.153.217] Use of uninitialized value in string ne at /usr/lib/perl5/site_perl/5.8.5/Bio/PrimarySeqI.pm line 372.
>>
>> --
>> Wes Barris <wes.barris at csiro.au>
>>
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> 
> 
> 


-- 
Wes Barris <wes.barris at csiro.au>