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MathOnco / NeoPredPipe

Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
GNU Lesser General Public License v3.0
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NeoRecoPo.py error #44

Closed h170607 closed 8 months ago

h170607 commented 8 months ago

Traceback (most recent call last): File "/data/yanr/script/neoantigen/NeoPredPipe-1.1/NeoRecoPo.py", line 135, in main() File "/data/yanr/script/neoantigen/NeoPredPipe-1.1/NeoRecoPo.py", line 124, in main preds.PerformCalculations(tmpOut, Options) File "/data/yanr/script/neoantigen/NeoPredPipe-1.1/StandardPredsClass.py", line 479, in PerformCalculations [neoantigens, samples] = self._compileNeoantigens(neofile, Options.Indels) File "/data/yanr/script/neoantigen/NeoPredPipe-1.1/StandardPredsClass.py", line 455, in _compileNeoantigens neoantigen = Neoantigen(nparams, indels) File "/data/yanr/script/neoantigen/NeoPredPipe-1.1/NeoClass.py", line 60, in init [res1, res2] = filter(lambda el: el[0] != el[1], zip(self.wtPeptide, self.mtPeptide))[0] TypeError: 'filter' object is not subscriptable

The columns names of my vcf files are as follows:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT tumor normal

The command is: python3 /data/script/neoantigen/NeoPredPipe-1.1/NeoPredPipe.py -I ./vcfs -H ./hlas.txt -o ./ -n TestRun -c 0 -E 8 9 10 -d python3 /data/script/neoantigen/NeoPredPipe-1.1/NeoRecoPo.py --neopred_in TestRun.neoantigens.txt --neoreco_out ./reco --fastas ./fastaFiles

h170607 commented 8 months ago

we used python 2 instead, and it worked, according to #39