[BioRuby] GFF3

[Naohisa GOTO]

On Mon, 16 Aug 2010 13:22:56 +0200
Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> On Fri, Aug 13, 2010 at 12:12:05AM +0900, Naohisa GOTO wrote:
> > > Now, to print FASTA I now do:
> > > 
> > >   gff3.sequences.each do | item |
> > >     print item.to_fasta(item.entry_id, 70)
> > >   end
> > 
> >  gff3.sequences.each do | item |
> >    print item.output(:fasta)
> >  end
> 
> As it stands, it is not a direct replacement as the entry_id gets
> printed twice. Also when I replace 

This is considered to be a bug.
The bug was reported previously, but was postponed.
http://lists.open-bio.org/pipermail/bioruby/2009-April/000897.html

> line 971: @sequences.collect { |s| s.to_fasta(s.entry_id, 70) }.join('')
> 
> with the output(:fasta) equivalent, the unit test in BioRuby fails,
> because the ID becomes 'test01 test01' instead of 'test01'.
> 
> Does it mean we have to modify 's', to get the proper output?
> 

The workaround is 
  s.output(:fasta, :header=>s.entry_id, :width=>70)

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org