From ea29c2b396f881ad160239d8c14cfff25c59489a Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Tue, 31 Dec 2019 13:55:40 -0500
Subject: [PATCH] update pan variants
---
.../models_class1_pan_variants/GENERATE.sh | 5 +++--
.../generate_hyperparameters.py | 9 ++++++++-
2 files changed, 11 insertions(+), 3 deletions(-)
diff --git a/downloads-generation/models_class1_pan_variants/GENERATE.sh b/downloads-generation/models_class1_pan_variants/GENERATE.sh
index a59365cc..82994301 100755
--- a/downloads-generation/models_class1_pan_variants/GENERATE.sh
+++ b/downloads-generation/models_class1_pan_variants/GENERATE.sh
@@ -66,10 +66,11 @@ then
python generate_hyperparameters.production.py > hyperparameters.production.yaml
python generate_hyperparameters.py hyperparameters.production.yaml no_pretrain > hyperparameters.no_pretrain.yaml
python generate_hyperparameters.py hyperparameters.no_pretrain.yaml single_hidden > hyperparameters.single_hidden_no_pretrain.yaml
+ python generate_hyperparameters.py hyperparameters.compact_peptide.yaml compact_peptide > hyperparameters.compact_peptide.yaml
python normalize_allele_names.py "$(mhcflurry-downloads path allele_sequences)/class1_pseudosequences.csv" --out allele_sequences.34mer.csv
fi
-for kind in 34mer_sequence single_hidden_no_pretrain no_pretrain
+for kind in 34mer_sequence single_hidden_no_pretrain no_pretrain compact_peptide
do
CONTINUE_INCOMPLETE_ARGS=""
if [ "$2" == "continue-incomplete" ] && [ -d "models.unselected.${kind}" ]
@@ -100,7 +101,7 @@ done
echo "Done training. Beginning model selection."
-for kind in single_hidden_no_pretrain no_pretrain 34mer_sequence
+for kind in single_hidden_no_pretrain no_pretrain 34mer_sequence compact_peptide
do
MODELS_DIR="models.unselected.${kind}"
mhcflurry-class1-select-pan-allele-models \
diff --git a/downloads-generation/models_class1_pan_variants/generate_hyperparameters.py b/downloads-generation/models_class1_pan_variants/generate_hyperparameters.py
index 75a363ac..8d9ea9bb 100644
--- a/downloads-generation/models_class1_pan_variants/generate_hyperparameters.py
+++ b/downloads-generation/models_class1_pan_variants/generate_hyperparameters.py
@@ -14,7 +14,7 @@ parser.add_argument(
help="Production (i.e. standard) hyperparameters grid.")
parser.add_argument(
"kind",
- choices=('single_hidden', 'no_pretrain'),
+ choices=('single_hidden', 'no_pretrain', 'compact_peptide'),
help="Hyperameters variant to output")
args = parser.parse_args(argv[1:])
@@ -38,9 +38,16 @@ def transform_to_no_pretrain(hyperparameters):
return [result]
+def transform_to_compact_peptide(hyperparameters):
+ result = deepcopy(hyperparameters)
+ result['peptide_encoding']['alignment_method'] = 'left_pad_right_pad'
+ return [result]
+
+
TRANSFORMS={
"single_hidden": transform_to_single_hidden,
"no_pretrain": transform_to_no_pretrain,
+ "compact_peptide": transform_to_compact_peptide,
}
transform = TRANSFORMS[args.kind]
--
GitLab