search

MathOnco / NeoPredPipe

Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
GNU Lesser General Public License v3.0
108 stars 29 forks source link

Docker version #42

Closed WuRAFY closed 3 months ago

WuRAFY commented 1 year ago

Thanks for the tool! I'm using docker version of NeoPredPipe, but I met the same error as #17.

Traceback (most recent call last):
  File "/software/NeoPredPipe-1.1/NeoPredPipe.py", line 523, in <module>
    main()
  File "/software/NeoPredPipe-1.1/NeoPredPipe.py", line 504, in main
    t.append(Sample(localpath, patname, patFile, hlas[patname], annPaths, netMHCpanPaths, pepmatchPaths, Options))
  File "/software/NeoPredPipe-1.1/NeoPredPipe.py", line 105, in __init__
    self.callNeoantigens(FilePath, netmhcpan, Options)
  File "/software/NeoPredPipe-1.1/NeoPredPipe.py", line 150, in callNeoantigens
    self.peptideFastas = MakeTempFastas(self.fastaChangeFormat, Options.epitopes)
  File "/software/NeoPredPipe-1.1/vcf_manipulate.py", line 147, in MakeTempFastas
    pos = int(seq_record.id.replace(";;",";").split(";")[6].split('-')[0])-1
IndexError: list index out of range

Can you please update docker version of the tool? Much thanks

elakatos commented 11 months ago

Thanks for the feedback, I'll update in the coming days!