From 73a1ce08750a4b9843b3d7b0297e3e150a915181 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Thu, 25 Jan 2018 19:49:14 -0500
Subject: [PATCH] update comment
---
downloads-generation/data_curated/GENERATE.sh | 4 ++++
downloads-generation/data_curated/curate.py | 4 ++--
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/downloads-generation/data_curated/GENERATE.sh b/downloads-generation/data_curated/GENERATE.sh
index 1f2b7067..11eb52ce 100755
--- a/downloads-generation/data_curated/GENERATE.sh
+++ b/downloads-generation/data_curated/GENERATE.sh
@@ -30,6 +30,7 @@ cd $SCRATCH_DIR/$DOWNLOAD_NAME
cp $SCRIPT_DIR/curate.py .
+# No mass-spec data
time python curate.py \
--data-iedb \
"$(mhcflurry-downloads path data_iedb)/mhc_ligand_full.csv.bz2" \
@@ -37,6 +38,9 @@ time python curate.py \
"$(mhcflurry-downloads path data_published)/bdata.20130222.mhci.public.1.txt" \
--out-csv curated_training_data.no_mass_spec.csv
+# With mass-spec data
+# Note that we STILL drop mass-spec data from IEDB here, since this data seems
+# low-quality.
time python curate.py \
--data-iedb \
"$(mhcflurry-downloads path data_iedb)/mhc_ligand_full.csv.bz2" \
diff --git a/downloads-generation/data_curated/curate.py b/downloads-generation/data_curated/curate.py
index fbb503a4..32f4a854 100755
--- a/downloads-generation/data_curated/curate.py
+++ b/downloads-generation/data_curated/curate.py
@@ -40,7 +40,7 @@ parser.add_argument(
default=[],
help="Path to Abelin Immunity 2017 mass-spec hits")
parser.add_argument(
- "--include-mass-spec",
+ "--include-iedb-mass-spec",
action="store_true",
default=False,
help="Include mass-spec observations in IEDB")
@@ -237,7 +237,7 @@ def run():
dfs = []
for filename in args.data_iedb:
- df = load_data_iedb(filename, include_mass_spec=args.include_mass_spec)
+ df = load_data_iedb(filename, include_mass_spec=args.include_iedb_mass_spec)
dfs.append(df)
for filename in args.data_kim2014:
df = load_data_kim2014(filename)
--
GitLab