[BiO BB] gff to sequence

[J Greenbaum]

I would suggest using the bioperl modules for parsing GFF and FASTA files:
Bio::Tools::GFF

and

Bio::SeqIO

This should save you a lot of pain.

-Jason

On Sat, Oct 3, 2009 at 5:59 AM, Mike Marchywka <marchywka at hotmail.com>wrote:

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> ----------------------------------------
> > Date: Sat=2C 3 Oct 2009 12:54:51 +0100
> > From: dan.bolser at gmail.com
> > To: bbb at bioinformatics.org
> > Subject: Re: [BiO BB] gff to sequence
> >
> > You can do this easily in Perl... Here is some 'pseudo code' to
> > (roughly) do it...
> >
> >
> > ## Get a hash of sequences=2C keys =3D IDs=2C values =3D sequence
> strings=
> =3B
> > my %sequences=3B
> > ...
> >
> > # open the GFF file ...
> >
> > while(my $gff =3D ){
> > my @gffcols =3D split(/\t/=2C $gff)=3B
> >
> > print substr($sequence{$gffcols[0]}=2C $gffcols[3]=2C $gffcols[4] -
> > $gffcols[3])=2C "\n"=3B
> > ...
> > }
> >
> >
> > Or something roughly similar to the above =3B-)
> >
> > Dan.
> >
> >
> > 2009/10/3 Kie Kyon Huang :
> >> Hi=2C
> >>
> >> Is there a way to quickly extract out the coordinates from a gff file
> >> and the corresponding sequence from a fasta file?
> >>
>
> I guess it depends what you mean by quick- quick to write you could use awk
> but then it depends what additional things you want to do with results.=20
> I ended up writing a C++ fasta utility program since PERL can slow down
> som=
> etimes but I ended up grabbing a couple of regex libraries to let me=20
> grep names etc.=20
>
>
>
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