[ensembl-dev] list of chromosomes in an organism

[Andrea Edwards]

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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