From c48e7a5302af5da09e6ad962b4c46695ec8c7192 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sat, 24 Feb 2018 16:02:59 -0500
Subject: [PATCH] update models_class1_selected_no_mass_spec to more closely
match models_class1
---
.../GENERATE.sh | 18 ++++--------------
1 file changed, 4 insertions(+), 14 deletions(-)
diff --git a/downloads-generation/models_class1_selected_no_mass_spec/GENERATE.sh b/downloads-generation/models_class1_selected_no_mass_spec/GENERATE.sh
index 5f6b50ae..da2c5f76 100755
--- a/downloads-generation/models_class1_selected_no_mass_spec/GENERATE.sh
+++ b/downloads-generation/models_class1_selected_no_mass_spec/GENERATE.sh
@@ -44,25 +44,15 @@ time python ./write_validation_data.py \
wc -l test.csv
-#time mhcflurry-predict \
-# test.csv \
-# --prediction-column-prefix "mhcflurry_unselected_" \
-# --models "$(mhcflurry-downloads path models_class1_unselected)/models" \
-# --out test.csv
-#wc -l test.csv
-
time mhcflurry-class1-select-allele-specific-models \
--data test.csv \
--models-dir "$(mhcflurry-downloads path models_class1_unselected)/models" \
--out-models-dir models \
- --scoring mse consensus \
+ --scoring combined:mse,consensus \
--consensus-num-peptides-per-length 10000 \
- --consensus-min-models 8 \
- --consensus-max-models 8\
- --mse-min-measurements 20 \
- --mse-min-models 8 \
- --mse-max-models 10000 \
- --num-jobs $(expr $PROCESSORS \* 2) --gpus $GPUS --max-workers-per-gpu 2 --max-tasks-per-worker 50
+ --combined-min-models 8 \
+ --combined-max-models 16 \
+ --num-jobs $(expr $PROCESSORS \* 2) --gpus $GPUS --max-workers-per-gpu 2 --max-tasks-per-worker 5
time mhcflurry-calibrate-percentile-ranks \
--models-dir models \
--
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