[ensembl-dev] Some Issues on Variation v64

Ma, Man Chun John manchunjohn-ma at uiowa.edu
Wed Oct 12 17:56:05 BST 2011


I just tried to make a script to make extract Variation synonyms from v64, and encountered the following issues:

1.  Variation::get_VariationFeature_by_dbID didn't seem to work using the following segment:

my $va=$registry->get_adaptor('rat','variation','variation');
my $vfa=$registry->get_adaptor('rat','variation','variationfeature');

print "Input: ENSRNOSNP971187\n";
my $one_snp=$va->fetch_by_name("ENSRNOSNP971187");
print "Ensembl Official name:", $one_snp->name, "\n";
my @synonyms=@{$one_snp->get_all_synonyms};
foreach (@synonyms){print "Synonym: ",$_, "\n";}
my $one_vf=$one_snp->get_VariationFeature_by_dbID;

which throwed:

-------------------- EXCEPTION --------------------
MSG: No dbID defined
STACK Bio::EnsEMBL::Variation::Variation::get_VariationFeature_by_dbID C:\ensemb
STACK toplevel HGVS-fetch-test.pl:21
Ensembl API version = 64

2. The output from VariationFeature:: get_all_hgvs_notations leaves a lot to be desired. The genomic HGVS notation for the above SNP would be 17:g.39585392T>C-- however, merely using "17" as a reference name is clearly inadequate as one cannot deduce what species' 17 does this refer to. I would consider RGSC3.4:17: g.39585392T>C a better alternative. On the other hand, the parameter $reference_name didn't seem to work.


John Ma
Kwitek Lab
Department of Pharmacology
University of Iowa
Iowa City, Iowa, USA

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