From beb4d69de2d46b611bf918cc8c2c4558e4cacc33 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 19 Feb 2018 14:42:02 -0500
Subject: [PATCH] Include IEDB mass spec in mass spec curated training data
---
downloads-generation/data_curated/GENERATE.sh | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/downloads-generation/data_curated/GENERATE.sh b/downloads-generation/data_curated/GENERATE.sh
index 11eb52ce..e2ba9187 100755
--- a/downloads-generation/data_curated/GENERATE.sh
+++ b/downloads-generation/data_curated/GENERATE.sh
@@ -39,8 +39,6 @@ time python curate.py \
--out-csv curated_training_data.no_mass_spec.csv
# With mass-spec data
-# Note that we STILL drop mass-spec data from IEDB here, since this data seems
-# low-quality.
time python curate.py \
--data-iedb \
"$(mhcflurry-downloads path data_iedb)/mhc_ligand_full.csv.bz2" \
@@ -50,6 +48,7 @@ time python curate.py \
"$(mhcflurry-downloads path data_systemhcatlas)/data.csv.bz2" \
--data-abelin-mass-spec \
"$(mhcflurry-downloads path data_published)/abelin2017.hits.csv.bz2" \
+ --include-iedb-mass-spec \
--out-csv curated_training_data.with_mass_spec.csv
bzip2 curated_training_data.no_mass_spec.csv
--
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