[ensembl-dev] get sequence from different build

[Jan-hinnerk Vogel]

Hi Stef,

ooops - it seems the tutorial is wrong, sorry. We'll correct it asap.

What happend is that the 'strand' argument, which should be the 5th  
argument, slipped somehow.
The assembly version should be the 6th argument, not the 5th. A good  
way to get warned about
those things is to  use perl -w or use 'use warnings' in your script -  
you see something like

"Argument "GRCh37" isn't numeric in integer multiplication (*) at /nfs/ 
ensembl/jhv//cvs_checkout//ensembl_live/modules/Bio/EnsEMBL/Mapper.pm  
line 314." so something is wrong ...


http://www.ensembl.org/info/docs/Pdoc/ensembl/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.html#POD15


You currently can't fetch sequence data from a different assembly  
version from the same database  - only the mapping is stored,
not the sequence of older assemblies. If you try it, you should get a  
string of NNNNN's back.

To fetch sequence for GRCh37 use the latest human core :  
homo_sapiens_core_59_37d
to fetch seq for NCBI36 you have to use an older database and connect  
with an older API checkout - ie homo_sapiens_core_***_36*


Hth,
            Jan-Hinnerk Vogel



==
Ensembl Genebuild Team Project Leader
www.ensembl.org



On 16 Sep 2010, at 12:54, mailsvl at fastmail.fm wrote:

> Hi,
>
> How can I get a slice from a different build then the default? When I
> try to compare GCRh37 and NCBI36 I keep getting the same sequences  
> (from
> GCRh37), no matter what region I try.

I assume you mean i "GRCh37" ?

>
> The code I use is from:
> http://www.ensembl.org/info/docs/api/core/core_tutorial.html
>
> Code:
> - $slice_adaptor->fetch_by_region( 'chromosome', '11', 123000000,
> 123000020, 'NCBI36' ); or
> - $slice_adaptor->fetch_by_region( 'chromosome', '11', 123000000,
> 123000020, 1, 'NCBI36' );
>
> Results when using ensembl website:
>> 11 dna:chromosome chromosome:NCBI36:11:123000000:123000020:1
> AAGAGTCCCACCAGCTCCAGG
>> 11 dna:chromosome chromosome:GRCh37:11:123000000:123000020:1
> TGCACTCCAGCCTGGGCAATG
>
> Thanks,
> Stef
> __________________
> http://www.fastmail.fm
>
>
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> Dev mailing list
> Dev at ensembl.org
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