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pdxgx / neoepiscope

predicts neoepitopes from phased somatic mutations detected using tumor/normal DNA-seq data
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Error when running Neoepiscope #15

Closed leldershaw closed 3 years ago

leldershaw commented 3 years ago

Error occurs after multiple warnings with message "Stop codon not detected prior to end of transcript {transcript_name}; this transcript may undergo degradation".

Neoepiscope version: 0.4.1

Command used: neoepiscope call -b GRCh38 -c Mel5_tumor_v_Mel5_normal.haplotypes.prepped -v Mel5_tumor_v_Mel5_normal.merged.vcf -o Mel5_tumor_v_Mel5_normal.neoepiscope.out -k 9 -p netMHCpan 4 affinity,rank -a HLA-A01:01,HLA-B08:01,HLA-C*07:01 --nmd --pp --trv --igv --allow-nonstart --allow-nonstop

Error message: Traceback (most recent call last): File "/home/ubuntu/anaconda3/bin/neoepiscope", line 8, in sys.exit(main()) File "/home/ubuntu/anaconda3/lib/python3.8/site-packages/neoepiscope/init.py", line 696, in main neoepitopes, fasta = get_peptides_from_transcripts( File "/home/ubuntu/anaconda3/lib/python3.8/site-packages/neoepiscope/transcript.py", line 3212, in get_peptides_from_transcripts peptides, protein = transcript_a.neopeptides( File "/home/ubuntu/anaconda3/lib/python3.8/site-packages/neoepiscope/transcript.py", line 2277, in neopeptides read_frame1 = self.reading_frame(seq[3]) File "/home/ubuntu/anaconda3/lib/python3.8/site-packages/neoepiscope/transcript.py", line 876, in reading_frame if pos > self._start_codon or pos < self._stop_codon: TypeError: '<' not supported between instances of 'int' and 'NoneType'

maryawood commented 3 years ago

Hi, thank you for pointing out this issue! We will be releasing a new version of neoepiscope soon, and I will address this issue in that release. I will let you know when that release is available!

maryawood commented 3 years ago

The new version of neoepiscope has been released! This version contains updates to the code to check whether the transcript has a stop codon prior to checking the stop codon position. Thanks again for pointing out this problem!