[ensembl-dev] Non-chromosomal download through api

[Patroklos Samaras]

Ok! problem solved! Your answers really helped! i just defined an array
with the chromosome names
so i just checkif the region name of the current slice exists! that's all!
then i save them as i wish!
Thanks for your time!

Patroklos

2012/10/7 Patroklos Samaras <patrik14 at gmail.com>

> 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
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>
>
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