Bio::Tools::GFF [Re: [Bioperl-l] Bio::SeqFeature::Generic]

[Jason Stajich]

I've got a fix - this code really needed to be written better.  I'm using
arrays and joins instead of chop-ing strings post-hoc.

Index: Bio/Tools/GFF.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/GFF.pm,v
retrieving revision 1.29
diff -r1.29 GFF.pm
570c570
<    my $valuestr;
---
>
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>    my @group;
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<        $str .= "\t"; # my interpretation of the GFF2
<                      # specification suggests the need
<                      # for this additional TAB character...??
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< 	   my $valuestr; # a string which will hold one or more values
< 	                 # for this tag, with quoted free text and
< 	                 # space-separated individual values.
---
> 	   my @v;
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< 		   $value = '"' . $value . '" '} # if the value contains
---
> 		   $value = '"' . $value . '" ';
> 	       }                                 # if the value contains
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< 	       $value = "\"\"" unless defined $value;
---
> 	       $value = '\""' unless defined $value;
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< 	       $valuestr .=  $value . " "; # with a trailing space in case
< 	                                   # there are multiple values
< 	       # for this tag (allowed in GFF2 and .ace format)
---
> 	       push @v, $value;
> 	       # for this tag (allowed in GFF2 and .ace format)
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< 	   $str .= "$tag $valuestr ; ";	# semicolon delimited with no '='
sign
---
> 	   push @group, "$tag ".join(" ", @v);
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<        chop $str; chop $str;  # remove the trailing semicolon and space
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>    $str .= "\t" . join(' ; ', @group);

-jason

-jason
On Wed, 22 Oct 2003, Heikki Lehvaslaiho wrote:

> Charles,
>
> Your code should be fine.
>
> I can see the extra spaces in the output by running the
> following script as 'gfftest.pl |od'.
>
> The method that needs changing is Bio::Tools::GFF::_gff2_string(), I'd
> rather have feedback from GFF people first. Lincoln or someone from his
> group should be able to say what is the correct way to solve this
> problem.
>
> Yours,
> 	-Heikki
>
> ---------------------gfftest.pl--------------------------------
> use Bio::Tools::GFF;
> use Bio::SeqFeature::Generic;
> use Data::Dumper;
>
> my $gffout = Bio::Tools::GFF->new(-gff_version => 2);
>
> my $feat = new Bio::SeqFeature::Generic();
> $feat->seq_id('111');
> $feat->source_tag('assembly');
> $feat->primary_tag('contig');
> $feat->start('1');
> $feat->end(123);
> $feat->add_tag_value('Contig','111');
> $gffout->write_feature($feat);
> #print Dumper $feat;
> --------------------------------------------------------
>
> On Tue, 2003-10-21 at 18:37, Charles Hauser wrote:
> > Don't know if this is a bug or a problem on my end.
> >
> > Using Bio::SeqFeature::Generic to generate gff:
> >
> > 	my $feat = new Bio::SeqFeature::Generic();
> > 	$feat->seq_id($seq->id);
> > 	$feat->source_tag('assembly');
> > 	$feat->primary_tag('contig');
> > 	$feat->start('1');
> > 	$feat->end($seq->length);
> > 	$feat->add_tag_value('Contig',$seq->id);
> > 	$out->write_feature($feat);
> >
> > I end up with 2 extra spaces following the group tag ('Contig
> > scaffold_1') which results in gbrowse returning: ...landmark not
> > recognized...
> >
> > deleting these spaces makes all right with the world.
> >
> > Is the problem in my code or in  Bio::SeqFeature::Generic?
> >
> > Charles
> >
> >
> > ______________________________________________________________________
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

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