[ensembl-dev] Retrieve gene flanking region question

[mr6 at ebi.ac.uk]

Hi Gregory,

With the slice adaptor, you can specify a flanking length for most features.

In your case, you can use
$slice_adaptor->fetch_by_gene_stable_id('ENSGxxx', 200)
This will return the slice of the corresponding gene as well as 200 base
pairs on the 5' and 3' ends.


Hope that helps,
Magali

> I am using API v74 and the v74 Human Core db. I obtain genes, transcripts
> and exons and then export fasta sequences for; gene flanking regions,
> UTRs, exons, introns.  I have found appropriate methods for everything
> except a simple method to obtain 5' and 3' gene flanking regions.
>
> Is there a method in the Core API that is similar to the Variation API
> method "$var->five_prime_flank_seq" ? I am using
> $slice_adaptor->fetch_by_region after calculating the desired flanking
> sequence coordinates given the gene start coordinate.
>
> Here is the code snippet that I am currently using.  The 5' flanking
> regions are correctly retrieved, but I wonder if there is a better way.
> Any suggestions are appreciated. Thank you.
> Greg Brown
>
> my $flank_size = 200;
> my $biotype = 'protein_coding';
> my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' );
> my @slices = @{ $slice_adaptor->fetch_all('toplevel') };  # toplevel or
> chromosome ?
> foreach my $slice (@slices) {
>    my $genes = $slice->get_all_Genes(undef,undef,1,undef,$biotype);  #
> Explicitly load transcripts and specify a biotype
> (default=protein_coding);
>    while ( my $gene = shift @{$genes} ) {
> 	my $gene_seq_region = $gene->slice->seq_region_name();
>        my $gene_start      = $gene->start() ;
>        my $gene_end        = $gene->end() ;
>        my $gene_strand     = $gene->strand();
>
> 	my $up_flank_start  = $gene_start - $flank_size;
>        my $up_flank_end    = $gene_start - 1;
>        my $down_flank_start = $gene_end + 1 ;
>        my $down_flank_end   = $gene_end + $flank_size;
>
>        my ($fiv_flank_start, $fiv_flank_end, $thr_flank_start,
> $thr_flank_end);
>        # Check strand and fix 5' and 3' directions according to strand
> direction
>        if ($gene_strand == "-1") {
>            $fiv_flank_start = $down_flank_start;
>            $fiv_flank_end   = $down_flank_end;
>            $thr_flank_start = $up_flank_start;
>            $thr_flank_end   = $up_flank_end;
>        }
>        else {
>            $fiv_flank_start = $up_flank_start;
>            $fiv_flank_end   = $up_flank_end;
>            $thr_flank_start = $down_flank_start;
>            $thr_flank_end   = $down_flank_end;
>        }
>
>        # There MUST be a better way to get flanking regions?  But this
> does work
>        my $fiv_flank_slice = $slice_adaptor->fetch_by_region( 'toplevel',
> $gene_seq_region, $fiv_flank_start, $fiv_flank_end, $gene_strand );
>        my $fiv_flank_seq   = $fiv_flank_slice->seq();
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>