[BioPerl] Re: [Bioperl-l] gff_string on an HSPI object is not Bio::DB::GFF friendly

Mark Wilkinson markw at illuminae.com
Fri Jan 9 10:50:28 EST 2004

On Fri, 2004-01-09 at 09:38, Jason Stajich wrote:

> So when you call $hsp->gff_string you are calling $hsp->query->gff_string.

not really.  If that were true, then the result of calling
$hsp->query->gff_string would be the same as calling $hsp->gff_string...
but the are not:

DB<17> p $hsp->query->gff_string
a101 BLASTN similarity 138 160 23 + 0 Bits "46.1";FracId 1;signif

DB<18> p $hsp->gff_string
a101 BLASTN similarity 138 160 23 + 0 Target gi|12329259 125209 125231

that was what I meant when I said that the individual sub-features are
not aware of each other...

I'll look at your search2gff code to see how you dealt with it; I'd much
rather see this implemented as a function than a standalone script,
since the latter isn't very portable.


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