[ensembl-dev] VEP 2.5 regex error in TranscriptVariationAllele.pm

Michael Yourshaw myourshaw at ucla.edu
Tue Jun 12 02:45:26 BST 2012


VCF input line:
19	42355761	.	C	CTAGAAA	2917.84	PASS	AC=2;AF=0.0076;AN=264;DP=11854;HRun=0;set=variant3-variant	GT:AD:DP:GQ:PL	...

in TranscriptVariationAllele.pm sub _check_for_peptide_duplication{

$self->{peptide} = ‘*K'
$hgvs_notation->{alt} = ‘*K’

error at line 1206 if($upstream_trans =~/$hgvs_notation->{alt}$/){

Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE K$/ at /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 1206, <GEN1> line 127.


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

This message is intended only for the use of the addressee and may contain information that is PRIVILEGED and CONFIDENTIAL, and/or may contain ATTORNEY WORK PRODUCT. If you are not the intended recipient, you are hereby notified that any dissemination of this communication is strictly prohibited. If you have received this communication in error, please erase all copies of the message and its attachments and notify us immediately. Thank you.





-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20120611/1910c7bd/attachment.html>


More information about the Dev mailing list