[ensembl-dev] Non-chromosomal download through api

Patroklos Samaras patrik14 at gmail.com
Sun Oct 7 20:42:50 BST 2012


By using fetch_all('toplevel') will the slices come ordered by region name?
i ask that because i want to have each slice to its chromosome**.txt
and the rest in some others.
The question is "Will chromosome 1 return in one slice? or in more?"

the unplaced scaffolds will surely be more than one slice (i realised that
from species as Takifugu)

Patroklos

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

> > my @slices = @{ $slice_adaptor->fetch_all('toplevel') };
> > i will get again the whole genome
>
> Exactly. I thought your point was to get slices for the whole genome,
> no? With fetch_all('toplevel') you are going to have both assembled
> chromosomes and whatever else is there unplaced. So you do not have to
> do fetch_by_region('chromsome') at all, as you are going to have both
> chromosomes and unplaced scaffolds with 'toplevel'.
>
> Sergei.
>
>
>
> On 7 October 2012 12:09, Patroklos Samaras <patrik14 at gmail.com> wrote:
> > 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
> >>
> >> land: +1 626 395 3593
> >>
> >> mobile: + 1 858 729 4531
> >>
> >> _______________________________________________
> >> Dev mailing list    Dev at ensembl.org
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> >
> >
> >
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>
>
>
> --
> Sergei (Siarhei Manakou) Manakov
>
> California Institute of Technology
> MC 147-75
>
> land: +1 626 395 3593
>
> mobile: + 1 858 729 4531
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
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