netMHCpan results are not parsed correctly in the output file

[StefTesta]

Hi,

I noticed that there is an issue with the latest release of the package. In the netMHC.py code line 45 should be changed from: if line.startswith(" 1 HLA"): to if re.match(r'^\s+1 HLA', line):

I am using netMHCpan 4.1.

Without these change the output file is empty.

[ysbioinfo]

Hi @StefTesta , Thank you for pointing it out. I am going to change this line in the next version to make it compatible with netMHCpan 4.1. In addition, since EL rank % is recommended by netMHCpan4.1, I will include the EL information into NeoSV output.

Yang

[alhafidzhamdan]

Hi there @ysbioinfo - great tool! I ran netMHCpan 4.1b on the test data and I got this error:

Loading SVs from test.sv.vcf.
106 SVs were detected.
22 duplicated SVs were removed
Preparing peptides for netMHC.
Running netMHC.
Filtering netMHC result by binding affinity.
Traceback (most recent call last):
  File "/exports/igmm/eddie/Glioblastoma-WGS/anaconda/envs/py37/bin/neosv", line 8, in <module>
    sys.exit(main())
  File "/exports/igmm/eddie/Glioblastoma-WGS/anaconda/envs/py37/lib/python3.7/site-packages/neosv/main.py", line 62, in main
    write_fusion(file_fusion, sv_fusions, dict_epitope)
  File "/exports/igmm/eddie/Glioblastoma-WGS/anaconda/envs/py37/lib/python3.7/site-packages/neosv/output.py", line 31, in write_fusion
    for allele in dict_neo[neoepitope]:
KeyError: 'EKDIDECALR'

Seems like not parsing it properly still. Could you please have a look? Thank you! A

[ysbioinfo]

Hi @alhafidzhamdan , Sorry that I missed this question. It should be caused by the compatibility with netMHCpan 4.1. I'll fix it in next version. Should be done by the end of Mar 2024. Hope this late reply be helpful to you.

Yang

[ysbioinfo]

The bug related to NetMHCpan4.1 should be fixed now. NetMHCpan4.0 is out of date and will not be supported by NeoSV.