[ensembl-dev] [SPAM] - Re: Core API problem - get_all_DBEntries - Email found in subject

Oliver, Gavin gavin.oliver at almacgroup.com
Fri Jan 21 15:13:39 GMT 2011


Thanks a lot Glenn.

Unrelated question but can you tell me how to get the start and end position of an exon relative to the gene (i.e. the start of the gene is position 1)?

I can do it fine for transcripts with exon->cdna_start(transcript).

Gavin

-----Original Message-----
From: glenn.ebi at googlemail.com [mailto:glenn.ebi at googlemail.com] On Behalf Of Glenn Proctor
Sent: 21 January 2011 15:05
To: Oliver, Gavin
Cc: dev at ensembl.org
Subject: [SPAM] - Re: [ensembl-dev] Core API problem - get_all_DBEntries - Email found in subject

Hi Gavin

This was actually a bug in
ensembl/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm - if you get the
HEAD version of that file you should be good to go.

We're also adding more intuitive aliases for get_all_DBLinks() and
get_all_DBEntries() in release 61 (due in few weeks).

Glenn.


On Fri, Jan 21, 2011 at 11:29 AM, Oliver, Gavin
<gavin.oliver at almacgroup.com> wrote:
> Hi,
>
>
>
> I am trying to use get_all_DBEntries with a wildcard.
>
>
>
> For example:
>
>
>
> my @dbentries = @{$gene->get_all_DBEntries("HGNC%")};
>
>
>
>
>
> The problem is it seems to return nothing.  If I use an exact serach term
> without wildcards it is fine however.
>
>
>
> Can someone advise?
>
>
>
> Gavin
>
>
>
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The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender.

Almac Group (UK) Limited, registered no. NI061368.  Almac Sciences Limited, registered no. NI041550.  Almac Discovery Limited, registered no. NI046249.  Almac Pharma Services Limited, registered no. NI045055.  Almac Clinical Services Limited, registered no. NI041905.  Almac Clinical Technologies Limited, registered no. NI061202.  Almac Diagnostics Limited, registered no. NI043067.  All preceding companies are registered in Northern Ireland with a registered office address of Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK.  

Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034. 

Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation.  More information on the Almac Group can be found on the Almac website: www.almacgroup.com






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