[ensembl-dev] Non-chromosomal download through api

[Patroklos Samaras]

Hi Sergei,
thanks for your answer!

I am getting the chromosomes with the following code
" my $slice_adaptor = $reg->get_adaptor( $ARGV[0], 'Core', 'Slice' );
my $slice = $slice_adaptor->fetch_by_region('chromosome', $ARGV[1]); "

i think that with
my @slices = @{ $slice_adaptor->fetch_all('toplevel') };
i will get again the whole genome

is there any way to get the rest of the genome (unplaced scaffolds) without
the sequences i've already downloaded?

Patroklos

2012/10/7 Sergei Manakov <siarheimanakov at gmail.com>

> hi Patroklos,
>
> If by non-chromosomal sequences you are referring to unplaced
> scaffolds (in GRCm38 those are called like GL456210.1, JH584292.1 and
> etc.), then slices for them as well as for regular chromosomes can be
> retrieved with this:
>
> my @slices = @{ $slice_adaptor->fetch_all('toplevel') };
>
>
> Sergei.
>
>
>
> On 7 October 2012 11:55, Patroklos Samaras <patrik14 at gmail.com> wrote:
> > Hi,
> > My name is Patroklos and i started using the Ensembl Api a few months
> ago to
> > download chromosomes etc.
> > Two days ago I realized that in this way I don't get the whole Genome -
> So I
> > need to download the non-chromosomal sequences too.
> > I looked through the tutorials and documentation but didn't really find
> > anything. Could anyone help me please?
> >
> > I'am using the 68 API version.
> >
> > Thanks in advance,
> > Patroklos
> >
> >
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>
>
> --
> Sergei (Siarhei Manakou) Manakov
>
> California Institute of Technology
> MC 147-75
>
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