[ensembl-dev] VEP uninitialized value errors and ignored tructural_variation_overlaps in VariationEffect.pm and VEP.pm

Michael Yourshaw myourshaw at ucla.edu
Thu May 24 01:46:30 BST 2012


With Ensembl version 67, cvs download 2012-05-22 and VEP v 2.5, I’m getting uninitialized value errors in VEP.pm and ignored tructural_variation_overlaps.

Examples of offending input VCF files are attached.

test_ab.vcf has two records, the second of which causes uninitialized value errors.

test_b.VCF has only the uninitialized value error-causing record. The problem here is that we don’t see the uninitialized value errors because the structural_variation_overlaps are being ignored (incorrectly or by design?).

Note that the uninitialized value errors occur when both records are present but not if either one is by itself in a one-record VCF.

The uninitialized value errors are associated with the 22	22569659	MERGED_DEL_2_105175 record, which is processed first by get_all_consequences.

Errors:
	Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 111, <GEN9> line 34.
	Use of uninitialized value in pattern match (m//) at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 111, <GEN9> line 34.
	Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 121, <GEN9> line 34.
	Use of uninitialized value in pattern match (m//) at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 121, <GEN9> line 34.
	Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 131, <GEN9> line 34.
	Use of uninitialized value in pattern match (m//) at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 131, <GEN9> line 34.
	Use of uninitialized value in string eq at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 142, <GEN9> line 34.
	Use of uninitialized value in pattern match (m//) at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm line 142, <GEN9> line 34.


The problem causing the uninitialized value errors is that $bvfoa->base_variation_feature->class_SO_term is undef.

The problem causing the code that generates the errors not to be executed when there is only one record in the VCF is:
	at VEP.pm whole_genome_fetch_sv line 2250
		if(defined($tr_cache->{$chr})) {
	When there is one variant in the VCF file, $tr_cache has no contents, and the code that pushes $svf->{structural_variation_overlaps} is not executed.
	When two variants are in the VCF file, $tr_cache has 6 transcripts under chr 22, the structural_variation_overlaps get pushed, and eventually the uninitialized value errors are emitted.



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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