From f21d9ebb7fa340a48f4b28bcec660050fec689e6 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sat, 25 Nov 2017 14:22:59 -0500
Subject: [PATCH] fix
---
downloads-generation/models_class1_experiments1/GENERATE.sh | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/downloads-generation/models_class1_experiments1/GENERATE.sh b/downloads-generation/models_class1_experiments1/GENERATE.sh
index 379a53f6..3afe151f 100755
--- a/downloads-generation/models_class1_experiments1/GENERATE.sh
+++ b/downloads-generation/models_class1_experiments1/GENERATE.sh
@@ -26,12 +26,12 @@ cd $SCRATCH_DIR/$DOWNLOAD_NAME
ALLELES="HLA-A*01:01 HLA-A*02:01 HLA-A*02:03 HLA-A*02:07 HLA-A*03:01 HLA-A*11:01 HLA-A*24:02 HLA-A*29:02 HLA-A*31:01 HLA-A*68:02 HLA-B*07:02 HLA-B*15:01 HLA-B*35:01 HLA-B*44:02 HLA-B*44:03 HLA-B*51:01 HLA-B*54:01 HLA-B*57:01"
# Standard architecture on quantitative only
-cp $SCRIPT_DIR/hyperparameters-standard.json .
+cp $SCRIPT_DIR/hyperparameters-standard.yaml .
mkdir models-standard-quantitative
time mhcflurry-class1-train-allele-specific-models \
--data "$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2" \
--only-quantitative \
- --hyperparameters hyperparameters-standard.json \
+ --hyperparameters hyperparameters-standard.yaml \
--out-models-dir models-standard-quantitative \
--percent-rank-calibration-num-peptides-per-length 0 \
--alleles $ALLELES &
@@ -43,7 +43,7 @@ do
mkdir models-${mod}
time mhcflurry-class1-train-allele-specific-models \
--data "$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2" \
- --hyperparameters hyperparameters-${mod}.json \
+ --hyperparameters hyperparameters-${mod}.yaml \
--out-models-dir models-${mod} \
--percent-rank-calibration-num-peptides-per-length 0 \
--alleles $ALLELES &
--
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