[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
ॐ
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
970.691.8299
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