[Bioperl-l] Blast to gff

[Ewan Birney]

On Mon, 18 Nov 2002, Wiepert, Mathieu wrote:

> Hi,
> 
> What's the simplest way to convert blast hits to gff?  I don't know
> why I thought there was a method somewhere to do this, is there one?

foreach $sf ( @blasthits ) {
	print $sf->gff_string(),"\n";
}

however, I suspect you will find the gff_string a little thin and almost
certainly not to the taste of what you want to feed it into (eg, Apollo or
whatever) - GFF is a very... open... standard.

It is pretty easy to roll your own with something like


  print join('\t','seq',$sf->primary_tag,'blast',$sf->start, etc





 > 
> -Mat
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