diff --git a/downloads-generation/models_class1_pan_refined/GENERATE.sh b/downloads-generation/models_class1_pan_refined/GENERATE.sh index fbb9f502fa2010bbf597f014b0f351aa080cb08d..b8d95720cf1c22038cd7a242a3e7cfb6a9875e22 100755 --- a/downloads-generation/models_class1_pan_refined/GENERATE.sh +++ b/downloads-generation/models_class1_pan_refined/GENERATE.sh @@ -63,13 +63,13 @@ time python make_multiallelic_training_data.py \ --hits "$(mhcflurry-downloads path data_mass_spec_annotated)/annotated_ms.csv.bz2" \ --expression "$(mhcflurry-downloads path data_curated)/rna_expression.csv.bz2" \ --exclude-contig "1" \ + --decoys-per-hit 1 \ --out train.multiallelic.no_chr1.csv time mhcflurry-multiallelic-refinement \ --monoallelic-data "$MONOALLELIC_TRAIN" \ --multiallelic-data train.multiallelic.no_chr1.csv \ --models-dir "$(mhcflurry-downloads path models_class1_pan)/models.with_mass_spec" \ - --max-models 1 \ --hyperparameters hyperparameters.yaml \ --out-affinity-predictor-dir $(pwd)/test_models.no_chr1.affinity \ --out-presentation-predictor-dir $(pwd)/test_models.no_chr1.presentation \ @@ -90,6 +90,7 @@ echo "Beginning production run" time python make_multiallelic_training_data.py \ --hits "$(mhcflurry-downloads path data_mass_spec_annotated)/annotated_ms.csv.bz2" \ --expression "$(mhcflurry-downloads path data_curated)/rna_expression.csv.bz2" \ + --decoys-per-hit 1 \ --out train.multiallelic.csv ALLELE_LIST=$(bzcat "$MONOALLELIC_TRAIN" | cut -f 1 -d , | grep -v allele | uniq | sort | uniq) diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml index 421c7e5e364d6e422058c4fc37f90dd528d5d95f..3fdcf338eb9f730d442a23b10eddfe6b509c6582 100644 --- a/mhcflurry/downloads.yml +++ b/mhcflurry/downloads.yml @@ -30,7 +30,7 @@ releases: default: false - name: models_class1_pan_refined - url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/models_class1_pan_refined.20191209.tar.bz2 + url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/models_class1_pan_refined.20191209b.tar.bz2 default: false - name: models_class1_pan_variants