You can do this easily in Perl... Here is some 'pseudo code' to
(roughly) do it...
## Get a hash of sequences, keys = IDs, values = sequence strings;
my %sequences;
...
# open the GFF file ...
while(my $gff = <GFF>){
my @gffcols = split(/\t/, $gff);
print substr($sequence{$gffcols[0]}, $gffcols[3], $gffcols[4] -
$gffcols[3]), "\n";
...
}
Or something roughly similar to the above ;-)
Dan.
2009/10/3 Kie Kyon Huang <[email protected]>:
> Hi,
>
> Is there a way to quickly extract out the coordinates from a gff file
> and the corresponding sequence from a fasta file?
>
> thanks
>
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