NERVE is an user-friendly software environment for the in silico identification of the best vaccine candidates from whole proteomes of bacterial pathogens. The purpose of this project is to update it, implementing new modules with machine learning based methods, and improving the performance of the already implemented ones.
License: MIT License
Control that the psortb parser reposrts the correct predictio. Unknown should be outputed for values <~ 7.5
A new fasta file parser should be created that does not cut input sequence names as SeqIO from Biopython does. SeqIO should be maintained and used just to validate input file format.
for a more user-friendly interface, you should make more visible the colab interface of Nerve located in the backup.py module
the threshold for deepfri should be 0.3
A module that reports the propensity of a sequence to bind to the principal human mhcII alleles should be implemented based on the api tool found here: http://tools.iedb.org/main/tools-api/
Use Uniprot api to retrieve protein names from protein uniprot accession codes (where present) and possibly show them in the result page.
Adjust rounding of conservation score and of PAD (which may lead to 1 as predicted value)
Api failure is observed when downloading some proteomes using uniprot API.
Hi all,
I run
user% ./NERVE.sh -epp False -vir True -rz True -p1 UP000000625 -wd /Users/ab/Applications/NERVE/docker/nerve/workdir/ecoli -g n -m True
and got :
wrote config file /root/.config/epitopepredict/default.conf
Start NERVE 2.0
10% done
20% done
30% done
40% done
50% done
60% done
70% done
80% done
90% done
trained model: HLA-A*01:01 3074 9
trained model: HLA-A*01:01 547 10
trained model: HLA-A*02:01 9805 9
trained model: HLA-A*02:01 3806 10
trained model: HLA-A*02:01 141 11
trained model: HLA-A*03:01 4569 9
trained model: HLA-A*03:01 1515 10
trained model: HLA-A*24:02 1668 9
trained model: HLA-A*24:02 456 10
trained model: HLA-B*07:02 3178 9
trained model: HLA-B*07:02 522 10
trained model: HLA-B*44:03 570 9
trained model: HLA-B*44:03 439 10
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
100% done
End NERVE computation successfully.
user%
but I don't find the results. I looked into my folder where is NERVE /Users/ab/Applications/NERVE/docker/nerve/workdir , but nothing. I also tried to set another folder by option -wd but again is empty.
Where are the results saved?
Please See the image and kindly instruct what to do in this kind problem. Why is the output file also wanting a file to be Fasta? If so how to fix it? I am trying to upload a Protein Sequence fasta file as input.
wrote config file /root/.config/epitopepredict/default.conf
Start NERVE 2.0
10% done
Traceback (most recent call last):
File "/usr/nerve_python/NERVE/code/NERVE.py", line 506, in
main()
File "/usr/nerve_python/NERVE/code/NERVE.py", line 358, in main
list_of_fasta_proteins, proteome1_new_path = quality_control(args.proteome1, args.working_dir, upload=True)
File "/workdir/code/Quality_control.py", line 127, in quality_control
fasta_list = is_fasta(path_to_fasta)
File "/workdir/code/Quality_control.py", line 103, in is_fasta
raise ValueError(f'{filename} is not in fasta format')
ValueError: /home/output/proteome1.fasta is not in fasta format
Use ReVac datasets do develop a PVC scoring system.
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