From 3cf3d6c39245293ffc1c78f6b8640ae9f6e48047 Mon Sep 17 00:00:00 2001 From: Sara Schulte <sara.schulte@hhu.de> Date: Mon, 9 Jan 2023 14:27:57 +0100 Subject: [PATCH] Update example arguments --- HOGVAX/example_arguments.txt | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/HOGVAX/example_arguments.txt b/HOGVAX/example_arguments.txt index f8b3dfe..6d73afd 100644 --- a/HOGVAX/example_arguments.txt +++ b/HOGVAX/example_arguments.txt @@ -1,3 +1,11 @@ -python hogvax.py --k 170 --outdir mhcI_unlinked --populations World --peptides ../OptiVax_Data/Peptides/optivax_unlinked_mhc1_4512_filtered_peptides.pep --allele-frequencies ../OptiVax_Data/Frequencies/IEDB_population_frequency2392_normalized.pkl --ba-threshold 0.638 --binding-affinities ../OptiVax_Data/BindingAffinities/25June_mhc1_netmhc-4.1_pred_affinity_pivot.pkl.gz --min-hits 1 --verbose 1 +# MHC I single allele frequencies +python hogvax.py --k 170 --outdir mhcI_unlinked --population World --peptides ../OptiVax_Data/Peptides/optivax_unlinked_mhc1_4512_filtered_peptides.pep --allele-frequencies ../OptiVax_Data/Frequencies/IEDB_population_frequency2392_normalized.pkl --ba-threshold 0.638 --binding-affinities ../OptiVax_Data/BindingAffinities/25June_mhc1_netmhc-4.1_pred_affinity_pivot.pkl.gz --min-hits 1 --verbose 1 -python hogvax.py --k 322 --outdir mhcII_unlinked --population World --peptides ../OptiVax_Data/Peptides/optivax_unlinked_mhc2_37435_filtered_peptides.pep -af ../OptiVax_Data/Frequencies/IEDB_population_frequency_mhc2_275normalized.pkl -t 0.638 -ba ../OptiVax_Data/BindingAffinities/25June_mhc2_netmhcii-4.1_pred_affinity_pivot_v1v2.pkl.gz --min-hits 1 --verbose 1 +# MHC I haplotypye frequencies +python hogvax.py --k 174 --outdir mhc1_robust --population White Black Asians --peptides ../OptiVax_Data/Peptides/optivax_unlinked_mhc1_4512_filtered_peptides.pep -af ../OptiVax_Data/Frequencies/haplotype_frequency_marry.pkl -t 0.638 -ba ../OptiVax_Data/BindingAffinities/all_mhc1_predictions_for_haplotypes.pkl.gz --min-hits 1 + +# MHC II single allele frequencies +python hogvax.py --k 322 --outdir mhc2_unlinked --population World --peptides ../OptiVax_Data/Peptides/optivax_unlinked_mhc2_37435_filtered_peptides.pep -af ../OptiVax_Data/Frequencies/IEDB_population_frequency_mhc2_275normalized.pkl -t 0.638 -ba ../OptiVax_Data/BindingAffinities/25June_mhc2_netmhcii-4.1_pred_affinity_pivot_v1v2.pkl.gz --min-hits 1 + +# MHC II haplotype frequencies +python hogvax.py --k 324 --outdir mhc2_robust --population White Black Asians --peptides ../OptiVax_Data/Peptides/optivax_unlinked_mhc2_haplotype_37435_filtered_peptides.pep -af .../OptiVax_Data/Frequencies/haplotype_frequency_marry2.pkl -t 0.638 -ba ../OptiVax_Data/BindingAffinities/all_mhc2_predictions_for_haplotypes.pkl.gz --min-hits 1 -- GitLab