Ensembl/VEP_plugins

Warning when running ProteinSeqs.pm

Opened this issue · 3 comments

shubham1637 commented

Hi I see a warning when running ProteinSeqs plugin. Is it possible to fix it?

(base) [shubham@cfx22885s-srcf-d11-20-east Variants]$ vep -i tumor_rna.vcf --plugin /path_to_ProteinSeq/ProteinSeqs.pm,reference=reference.fa,mutated=mutated.fa --dir_cache /path_to_cache/VEPcache --offline 
Use of /c modifier is meaningless without /g at (eval 42) line 2.
WARNING: Failed to compile plugin /path_to_ProteinSeq/ProteinSeqs.pm: Search pattern not terminated at (eval 42) line 2.

I also do not see the output reference.fa and mutated.fa files

nakib103 commented

Hello @shubham1637,

Thanks for your query!

Can you mention the Perl and VEP version you are using?
Also, can you provide the input you are using, it will help re-produce the issue.

Best regards,
Nakib

shubham1637 commented

I am using a computing cluster and I only load ensembl-vep/113.3. So cannot find out the perl version.
But the problem got solved when I used --plugin /path_to_ProteinSeq/ProteinSeqs instead of ProteinSeqs.pm

I was wondering does Downstream give fasta output? I could not find any. I only got output.txt
vep -i tumor.vcf --safe --plugin Downstream --offline -o output.txt --fasta path_to_fasta
This is the header and first row of the txt file:

#Uploaded_variation     Location        Allele  Gene    Feature Feature_type    Consequence     cDNA_position   CDS_position    Protein_position        Amino_acids     Codons  Existing_variation      Extra
chr1_16841_G/T  chr1:16841      T       ENSG00000223972 ENST00000450305 Transcript      downstream_gene_variant -       -       -       -       -       -       IMPACT=MODIFIER;DISTANCE=3171;STRAND=1
nakib103 commented

ProteinSeqs

You cannot give "/path_to_ProteinSeq/ProteinSeqs" or "ProteinSeqs.pm" with the .pm. You should use only the plugin name and the command should be like this -

--plugin ProteinSeqs,reference=reference.fa,mutated=mutated.fa

The plugin module needs to be in the Perl library path so that VEP can find it. See more at -
https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#plugins_use

Downstream
The Downstream plugin does not give fasta output. It includes DownstreamProtein and ProteinLengthChange field in the VEP output file providing the changed peptide sequence and length respectively for a frameshift variant. The following is a good example -

#Uploaded_variation	Location	Allele	Gene	Feature	Feature_type	Consequence	cDNA_position	CDS_position	Protein_position	Amino_acids	Codons	Existing_variation	Extra
rs1553314015	1:230710048	-	ENSG00000135744	ENST00000366667	Transcript	frameshift_variant	843	776	259	M/X	aTg/ag	-	IMPACT=HIGH;STRAND=-1;DownstreamProtein=REPVWTAPWLSTPTSTSKGR;ProteinLengthChange=-197