[BioRuby] GFF3
Pjotr Prins
pjotr.public14 at thebird.nl
Mon Aug 16 11:22:56 UTC 2010
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
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?
Pj.
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