[ensembl-dev] how to calculate transcript length ?

[Thibaut Hourlier]

Hi,
I would recommend you to use the Perl API for all the information you 
want to retrieve from Ensembl.
It's quite easy to use and if there is a schema change, you will not 
have to change all your SQL queries.
Here is some documentation:
http://www.ensembl.org/info/docs/api/core/core_tutorial.html
http://www.ensembl.org/info/docs/Doxygen/core-api/index.html
http://www.ensembl.org/info/docs/api/index.html

Here is some code for your query:

use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
     -host => 'ensembldb.ensembl.org', # alternatively 'useastdb.ensembl.org'
     -user => 'anonymous'
);
my $gene_adaptor  = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
my $gene = $gene_adaptor->fetch_by_stable_id('ENSG00000089234');
foreach my $transcript (@{$gene->get_all_Transcripts()) {
   print STDOUT 'Length of ', $transcript->display_id, ': ', $transcript->length, "\n";
}

Regards
Thibaut

On 31/07/12 12:49, Jay Humphrey wrote:
> Length is end - start + 1.
> 1 2 3 [4 5 6 7 8] 9
> start = 4, end = 8
> 8 - 4 = 4, actually there are 5 residues.
>
> On 31/07/2012 10:39, ?? wrote:
>> Hi All
>> I wondering how to calculate transcript length within Ensembl database.
>> I try to sum exon's length:
>>
>> SELECT tp.stable_id, SUM( e.seq_region_end ) - SUM( e.seq_region_start )
>> FROM gene g
>> JOIN transcript tp ON ( g.gene_id = tp.gene_id )
>> JOIN exon_transcript et ON ( et.transcript_id = tp.transcript_id )
>> JOIN exon e ON ( e.exon_id = et.exon_id )
>> WHERE g.stable_id = 'ENSG00000089234'
>> GROUP BY tp.stable_id
>>
>> But the result is inconsistent with Ensembl official data:
>> http://asia.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000089234;r=12:112080797-112123790
>>
>> If you know how to dig out the datas of 
>> variation,orthologue,paralogue,regulation. please also tell me.
>>
>>
>> Thanks million
>> -- 
>> Gang Chen
>> TILSI
>> Taicang Institute For Life Science Information
>> Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu 
>> Province, P.R.China
>> Phone: (+86)512-82782588
>>
>>
>>
>> _______________________________________________
>> Dev mailing listDev at ensembl.org
>> List admin (including subscribe/unsubscribe):http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog:http://www.ensembl.info/
>
> -- 
> Jay Humphrey                   Ensembl Genomes Web Developer
> EMBL-EBI                       Tel: +44-(0)1223-492682
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UKhttp://www.ensemblgenomes.org/  
>
>
> _______________________________________________
> Dev mailing listDev at ensembl.org
> List admin (including subscribe/unsubscribe):http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog:http://www.ensembl.info/


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