X-lab-3D / PANDORA

MODELLER-based, anchor restrained, Peptide-MHC Modelling pipeline
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missing file: allelenames #249

Closed cbaakman closed 1 year ago

cbaakman commented 1 year ago

I've installed pandora using miniconda and downloaded the database using install_database. I also installed netMHCpan. I'm running PANDORA like this:

from PANDORA.Wrapper.Wrapper import Wrapper
from PANDORA.Database import Database

if __name__ == "__main__":

    db = Database.load('/projects/0/einf2380/softwares/PANDORA_databases/default/PANDORA_database.pkl')

    wrapper = Wrapper("/home/baakmanc/iedb-mhc-ligand-classI-seq-data.csv", header=True, MHC_class="I",
                      delimiter=',',
                      IDs_col=0, peptides_col=2, allele_name_col=1, M_chain_col=4,
                      use_netmhcpan=True,
                      verbose=True, database=db, num_cores=128,
                      collective_output_dir='/projects/0/einf2380/data/iedb-models/')

However, empty directories are created. Closer inspection of the output shows that the following is thrown:

FileNotFoundError: [Errno 2] No such file or directory: '/home/baakmanc/miniconda3/envs/pandora/bin/data/allelenames'

Where can I get the file named allelenames ?

cbaakman commented 1 year ago

It appeared that this file needed to be downloaded here: https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/data.tar.gz