[ensembl-dev] update API issue

Fri Nov 15 19:37:46 GMT 2013

Hi,

I've run your code with APOM and got back the following

APOM:ENSG00000204444:6:31620193:31625987,
APOM:ENSG00000235754:HSCHR6_MHC_SSTO:31610134:31615927,
APOM:ENSG00000206409:HSCHR6_MHC_QBL:31610434:31616227,
APOM:ENSG00000231974:HSCHR6_MHC_MANN:31659685:31665479,
APOM:ENSG00000224290:HSCHR6_MHC_COX:31607608:31613401,
APOM:ENSG00000227567:HSCHR6_MHC_DBB:31602375:31608169,
APOM:ENSG00000226215:HSCHR6_MHC_MCF:31696476:31702270,

I'm really not seeing how you're managing to come to this location using the code you've sent in. In fact if you look at the website for APOM on MHC_MCF it's at position 31696476-31702270.

http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000226215;r=HSCHR6_MHC_MCF:31696476-31702270

Are you trying to project the feature to a lower level? I've attached the script with some minor modifications to ensure it can run (there were some issues) so you can confirm that I'm running the right thing. Is there any other code you're not sharing with us?

Andy

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On 15 Nov 2013, at 19:10, Nathalie Conte <nconte at ebi.ac.uk> wrote:

> hi, sure
> example there
> APOM:ENSG00000226215:HSCHR6_MHC_MCF_CTG1:2999873:3005667,
> thanks
> Nat
> On 15 Nov 2013, at 16:53, Andy Yates <ayates at ebi.ac.uk> wrote:
> 
>> Hi,
>> 
>> Sorry could you send a HGNC symbol that causes the error please? I've tried with a number of symbols including BRAF, BRCA2, ABO & HCG21 none of which show the behaviour you're seeing. In fact running the code for HCG21 gives me:
>> 
>> HCG21:ENSG00000233529:6:30913756:30922639,
>> 
>> If I take out the test for $gene->slice->is_reference() I get:
>> 
>> HCG21:ENSG00000233529:6:30913756:30922639,
>> HCG21:ENSG00000235747:HSCHR6_MHC_DBB:30904474:30913356,
>> HCG21:ENSG00000230541:HSCHR6_MHC_QBL:30903331:30912213,
>> HCG21:ENSG00000223454:HSCHR6_MHC_COX:30903456:30912338,
>> HCG21:ENSG00000228448:HSCHR6_MHC_MCF:30992301:30992681,
>> 
>> I'm just not seeing the issue you're reporting. Also the sequence region name you gave is not a toplevel sequence. As you can see from this output HSCHR6_MHC_MCF is the toplevel region; HSCHR6_MHC_MCF_CTG1 is an underlying supercontig and is *not* a toplevel region. We only use the non-reference attribute when working with toplevel sequence regions. That's why calling is_reference() on a slice pointing at HSCHR6_MHC_MCF_CTG1
>> 
>> Andy
>> 
>> 
>> On 15 Nov 2013, at 15:54, nconte at ebi.ac.uk wrote:
>> 
>>> HI,
>>> This is the bit of the code which will get the is_reference test-
>>> if you replace $Ggene with any gene symbol from HGNC this should work.
>>> #!/usr/local/bin/perl
>>> use strict;
>>> use warnings;
>>> 
>>> use Bio::EnsEMBL::Registry;
>>> 
>>> Bio::EnsEMBL::Registry->load_registry_from_db(
>>> 	-host=>"ensembldb.ensembl.org", -user=>"anonymous",
>>>       -port=>'5306', 'db_version' => 73,);
>>> my $gene_adaptor=Bio::EnsEMBL::Registry->get_adaptor( 'human', 'Core',
>>> 'Gene' );
>>> 
>>> 
>>> my $all_genes=$gene_adaptor->fetch_all_by_external_name($Ggene,'HGNC'); #
>>> this is where I capture the ensembl genes from each key
>>> #######
>>> if (!scalar (@{$all_genes})) {print  $Ggene.'no ensembl gene object
>>> ',"\t","no ensembl variation no object","\t","no ensembl orthologues no
>>> object","\t"; next; } elsif  (scalar (@{$all_genes})){
>>> 	 foreach my $gene (@{$all_genes}){
>>> if (!$gene){print $Ggene.' '. 'no_ensembl_gene'; next} elsif
>>> 	 ( $gene && $gene->slice->is_reference ) {
>>> # no  genes which are on patches are removed only the ref assembly are
>>> kept , -!!!!
>>> #print   'GWAS_gene2: '.$Ggene,  "\t",defined($gene->external_name) ?
>>> print   defined($gene->external_name) ?
>>> $gene->external_name :'no_ensembl_gene',":", defined($gene->stable_id) ?
>>> $gene->stable_id : 'no_stableID',":", defined($gene->seq_region_name) ?
>>> $gene->seq_region_name:
>>> 'no_seq_region_name:',":",defined($gene->seq_region_start) ?
>>> $gene->seq_region_start:
>>> 'no_seq_region_start',":",defined($gene->seq_region_end) ?
>>> $gene->seq_region_end: 'no_seq_region_end',"," ;}
>>> 
>>> Thanks
>>> 
>>> Nat
>>> 
>>>> Hi there,
>>>> 
>>>> A reference sequence is detected by the non-existence of a non_ref flag in
>>>> seq_region_attrib. I've done this query in 73:
>>>> 
>>>> select *
>>>> from seq_region sr
>>>> join seq_region_attrib sra using (seq_region_id)
>>>> join attrib_type a using (attrib_type_id)
>>>> where sr.name = 'HSCHR6_MHC_MCF_CTG1'
>>>> and a.code = 'non_ref'
>>>> 
>>>> And have got no rows back suggesting that $gene->slice->is_reference()
>>>> when slice is HSCHR6_MHC_MCF_CTG1 will return false. Could you send us
>>>> your code please?
>>>> 
>>>> Andy
>>>> 
>>>> On 15 Nov 2013, at 14:26, nconte at ebi.ac.uk wrote:
>>>> 
>>>>> Hi,
>>>>> I have been updating my ensembl API versions from 71 to 73 today, and
>>>>> reran a script to test it was working.
>>>>> In my script I am excluding genes  Ids for haplotypes /  LRG /
>>>>> pseudoautomosal
>>>>> or  assembly patches/fixes regions. I am using this test/method to
>>>>> exclude
>>>>> them
>>>>> (if $gene->slice->is_reference)
>>>>> 
>>>>> I am now getting genes mapping on HSCHR6_MHC_MCF_CTG1 which were
>>>>> excluded
>>>>> on my last version of the API. Is the slice->is_reference deprecated?
>>>>> Thanks
>>>>> Nathalie
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Dev mailing list    Dev at ensembl.org
>>>>> Posting guidelines and subscribe/unsubscribe info:
>>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>>> Ensembl Blog: http://www.ensembl.info/
>>>> 
>>>> 
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>>> 
>>> 
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>> 
>> 
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> 
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