[ensembl-dev] VEP.pm error in svf_to_consequences

Michael Yourshaw myourshaw at ucla.edu
Thu Apr 19 21:27:25 BST 2012

VEP 2.4 fails with this error:
Can't locate object method "stable_id" via package "Bio::EnsEMBL::Funcgen::MotifFeature" at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 1123, <GEN1> line 5028.

There is no $feature->stable_id

$feature_type = MotifFeature (this variant also throws Gene, Transcript, and RegulatoryFeature feature_types that have stable ids).
$feature is a Bio::EnsEMBL::Funcgen::MotifFeature
$feature contains (inter alia):
	dbID = 618345 
	display_label = PU1:MA0080.1
	end = 39460062
	interdb_stable_id = undef
	score = 1
	slice (looks like all of chr 22?)
	start = 39460057
	strand = 1

This looks like it might be a data error. It is the only such error on chr 22 of the 1000 genomes data, but there may be more in the other chromosomes.

My temporary fix in VEP.pm:
        my $base_line = {
            Feature_type     => $feature_type,
            Feature          => $feature->can('stable_id') ? $feature->stable_id : undef,
            #cDNA_position    => format_coords($svo->cdna_start, $svo->cdna_end),
            #CDS_position     => format_coords($svo->cds_start, $svo->cds_end),
            #Protein_position => format_coords($svo->translation_start, $svo->translation_end),

The input VCF line (exerpted from 1000 Genomes) start with:
22	39432459	MERGED_DEL_2_106019	TGGAAGC …

See attached file for the whole line

Michael Yourshaw
UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu

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