[Bioperl-l] GFF file output missing semicolon

[Wes Barris]

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???

-- 
Wes Barris
E-Mail: Wes.Barris at csiro.au