From 9bff103995c03dc02afaabda057f9a8a5870d51c Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Tue, 10 Dec 2019 11:49:36 -0500
Subject: [PATCH] fix
---
downloads-generation/models_class1_pan_refined/GENERATE.sh | 3 ++-
mhcflurry/downloads.yml | 2 +-
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/downloads-generation/models_class1_pan_refined/GENERATE.sh b/downloads-generation/models_class1_pan_refined/GENERATE.sh
index fbb9f502..b8d95720 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 421c7e5e..3fdcf338 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
--
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