[ensembl-dev] core API question
nconte at ebi.ac.uk
nconte at ebi.ac.uk
Fri Jul 19 15:27:50 BST 2013
HI,
I am fetching ensembl genes from HGNC gene list using the core API
I am using these methods below to fetch ensembl gene objects from my HGNC
Ids called $key:
my $all_genes=$gene_adaptor->fetch_all_by_external_name($key,'HGNC');
#then I am parsing through my gene reflist to get gene related attributes
print OUTFILE2 $key, "\t",$value, "\t",defined($gene->external_name) ?
'map with '. scalar (@{$all_genes}). ' ensembl_gene(s):
'.$gene->external_name :'no_ensembl_gene',"\t", defined($gene->stable_id)
? $gene->stable_id : 'no_stableID', "\n";
for some genes I get ensmebl Ids for haplotypes or LRG or pseudoautomosal
or assembly patches/fixes regions. see below
AIF1 1 map with 6 ensembl_gene(s): AIF1 ENSG00000206428
AIF1 1 map with 6 ensembl_gene(s): AIF1 ENSG00000235985
AIF1 1 map with 6 ensembl_gene(s): AIF1 ENSG00000234836
AIF1 1 map with 6 ensembl_gene(s): AIF1 ENSG00000237727
AIF1 1 map with 6 ensembl_gene(s): AIF1 ENSG00000204472
AIF1 1 map with 6 ensembl_gene(s): AIF1 ENSG00000235588
I will like only to get the GRCh37 gene IDs with chr:start-end
coordinates.In the abose example, only ENSG00000204472. Is there a clever
way to do this using a API method, or my only chance is to test the
$gene->seq_name content?
many thanks
Nathalie
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