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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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vcf_manipulate.py #3

Closed ChengYunazhi closed 5 years ago

ChengYunazhi commented 5 years ago

INFO: Annovar reference files of build hg19 were given, using this build for all analysis. INFO: Begin. INFO: Proper directory already exists. Continue. INFO: Proper directory already exists. Continue. INFO: Proper directory already exists. Continue. INFO: Proper directory already exists. Continue. INFO: ANNOVAR Ready files for XXX already present. INFO: ANNOVAR Annotation files for XXXX already present. INFO: Coding change fasta files for XXXX already present. INFO: Coding change fasta files XXXX has already been reformatted. Traceback (most recent call last): File "/DataProcess/softwares/NeoPredPipe-1.0/main_netMHCpan_pipe.py", line 456, in main() File "/DataProcess/softwares/NeoPredPipe-1.0/main_netMHCpan_pipe.py", line 441, in main t.append(Sample(localpath, patname, patFile, hlas[patname], annPaths, netMHCpanPaths, pepmatchPaths, Options)) File "/DataProcess/softwares/NeoPredPipe-1.0/main_netMHCpan_pipe.py", line 94, in init self.callNeoantigens(FilePath, netmhcpan, Options) File "/DataProcess/softwares/NeoPredPipe-1.0/main_netMHCpan_pipe.py", line 138, in callNeoantigens self.peptideFastas = MakeTempFastas(self.fastaChangeFormat, Options.epitopes) File "/DataProcess/softwares/NeoPredPipe-1.0/vcf_manipulate.py", line 138, in MakeTempFastas pos = int(seq_record.id.replace(";;",";").split(";")[6])-1 ValueError: invalid literal for int() with base 10: '493-494'

rschenck commented 5 years ago

Can you please verify that the example data works for you?

Further, can you please provide an example of the vcf you are using or the change Fasta file?

ChengYunazhi commented 5 years ago

example data works well. I found error was caused by "insertion" type in seq ID in fasta file, after change code in line 138, error was fixed. Thanks!

rschenck commented 5 years ago

Okay. Indels are currently not supported for the released version, but within the next couple of weeks we will be pushing a fix to include this. The problem for indels is the calculation of the Neoantigen recognition potentials. Currently NeoPredPipe should be filtering all indels.

elakatos commented 5 years ago

We have now updated the repository, and support for Indels (and any other frameshift type mutations) is included in the master branch. In the most recent version variants such as the above are considered for a separate XXX.neoantigens.Indels.txt and summary table. Let me know if there is still an issue with processing of the Annovar output.