[ensembl-dev] list of chromosomes in an organism

[Anne Parker]

There is no Y chromosome in the cow genome, because the reference  
genome is female :)

On 12 Nov 2010, at 14:52, Andrea Edwards wrote:

> Hi
>
> I made a mistake in my last message, wasn't concentrating. I should  
> have said:
>
> I have got a list of the chromosomes
> in the cow genome using the perl API and the 'Y' chromosome is named  
> MT. However I can't retrieve this chromosome using either of the  
> following
>
> $slice = $slice_adaptor->fetch_by_region('chromosome','Y');
> $slice = $slice_adaptor->fetch_by_region('chromosome','MT');
>
> The $slice is undefined
>
> I did this workaround to get chromsomes 1-29, X and MT
>
> @slices = @{ $slice_adaptor->fetch_all('chromosome') };
> foreach $slice (@slices) {
>
>    unless ($slice->seq_region_name() =~ /Un/) {
>        .....
>    }
> }
>
> But i was curious why I couldn't get MT directly
>
> thanks
>
>
> On 12/11/2010 14:36, Andrea Edwards wrote:
>> hi
>>
>> how do you get the list of chromosomes in an organism via the perl  
>> api?
>>
>> I ask because I'm trying to get the cow Z chromosome and can't  
>> access it. It is labelled MT in the genome browser so I have tried
>>
>> $slice = $slice_adaptor->fetch_by_region('chromosome','Z');
>> $slice = $slice_adaptor->fetch_by_region('chromosome','MT');
>>
>> and neither work
>>
>> Thanks a lot
>>
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>
>
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Anne Parker
Ensembl Web Production Manager
http://www.ensembl.org