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ambj / MuPeXI

MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.
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Reference Files for the given example VCF #40

Open ALogandha opened 3 years ago

ALogandha commented 3 years ago

Hi,

I am trying to run MuPeXi on the given example VCF (https://raw.githubusercontent.com/ambj/MuPeXI/master/data/example.vcf) using the below command but end up with error:

MuPeXI.py -v data/example.vcf -a HLA-A01:01,HLA-A02:02

I am using homo_sapiens_refseq_vep_104_GRCh38.tar.gz for VEP cache (http://ftp.ensembl.org/pub/release-104/variation/indexed_vep_cache/homo_sapiens_vep_104_GRCh38.tar.gz) and fasta files downloaded from http://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens as the reference.

Please find the error message pasted below:

Reading in data Creating proteome reference dictionary Traceback (most recent call last): File "MuPeXI/MuPeXI.py", line 1800, in main(sys.argv[1:]) File "MuPeXI/MuPeXI.py", line 44, in main proteome_reference, sequence_count = build_proteome_reference(paths.proteome_reffile, input.webserver, species) File "MuPeXI/MuPeXI.py", line 280, in build_proteome_reference proteome_reference[geneID][transID] += line.strip() UnboundLocalError: local variable 'geneID' referenced before assignment

Could I request you to confirm I am using the correct references to run the example VCF?

I appreciate your help!

Thanks in advance.

Regards, Ashmitaa.

zyxNo1 commented 7 months ago

I have the same question. Any idea?