[Bioperl-l] GFF file output missing semicolon

[Jason Stajich]

I think that the gff2 dumping was not particularly good - I think I made
some fixes to clean it up on the main trunk in the last few months.  I can
certainly dump with Tools:GFF and load into Gbrowse just fine with
the current code.  Wes you might try with bioperl 1.3.x series
Bio::Tools::GFF instead.

-jason

On Fri, 21 Nov 2003, Lincoln Stein wrote:

> Hi,
>
> The GFF2 spec specifies that the semicolon separates tag/value pairs.  It does
> not say that the last tag/value should be terminated by a semicolon.  It also
> specifies that any amount of whitespace can occur around the semicolon.
>
> Lincoln
>
> On Thursday 20 November 2003 11:19 pm, Wes Barris wrote:
> > Hi,
> >
> > I have written a bioperl program that parses blast files and generates
> > a gff file.  I have everything working except there is one small detail
> > that I have not been able to figure out.  When generating each line
> > of gff output, the semicolon is left off at the end of the Accession
> > name.  Here is a sample line from a gff file that I generated:
> >
> > AF354168        mirseeker       pred_miRNA      188152  188251  198     -
> >    . Note "mirseeker score 17.58"   ; Accession
> > "s-h_19_r_99330000-99363000"
> >
> > Notice that:
> >
> > 1) There are three space characters after the note and the semicolon
> >     that occurs before "Accession".
> >
> > 2) At the end of the line, after the Accession, there are three space
> >     characters and no semicolon.  Without that semicolon, the genome
> >     browser doesn't display the "rollover" information properly.
> >
> > 3) The "Note" field is written before the "Accession" field.  I thought
> >     that the Accession should come first.
> >
> > Here is the relevant portion of my code:
> >
> >        while( my $hsp = $hit->next_hsp ) {
> >           my $strand = 1;
> >           $strand = -1 if ($hsp->strand('query') == -1 ||
> > $hsp->strand('hit') == -1); my $feature = new Bio::SeqFeature::Generic(
> >                          -source_tag=>$source,
> >                          -primary_tag=>$feature_type,
> >                          -start=>$hsp->start('hit'),
> >                          -end=>$hsp->end('hit'),
> >                          -score=>$hit->raw_score,
> >                          -strand=>$strand,
> >                          -tag=>{
> >                                  Accession=>$result->query_name,
> >                                  Note=>$result->query_description,
> >                                  }
> >                          );
> >           $feature->seq_id($hit->accession);
> >           $gffio->write_feature($feature);       #Bio::SeqFeatureI
> >        }
> >
> > Perhaps I am not adding the "Accession" and "Note" fields properly???
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu