[ensembl-dev] Non-chromosomal download through api

Sergei Manakov siarheimanakov at gmail.com
Sun Oct 7 20:20:04 BST 2012


> 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
>>
>> _______________________________________________
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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




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