From 0805397e0e1884f1f822675acd4be271ade3c086 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sun, 6 Oct 2019 21:46:41 -0400
Subject: [PATCH] fix
---
.../data_mass_spec_benchmark/GENERATE.sh | 55 +++++++++----------
.../run_predictors.py | 16 ++++--
2 files changed, 39 insertions(+), 32 deletions(-)
diff --git a/downloads-generation/data_mass_spec_benchmark/GENERATE.sh b/downloads-generation/data_mass_spec_benchmark/GENERATE.sh
index f42013b3..fbb1db71 100755
--- a/downloads-generation/data_mass_spec_benchmark/GENERATE.sh
+++ b/downloads-generation/data_mass_spec_benchmark/GENERATE.sh
@@ -98,8 +98,7 @@ fi
# Write out and process peptides.
# First just chr1 peptides, then all peptides.
# TODO: switch this back
-#for subset in chr1 all
-for subset in all chr1
+for subset in chr1 all
do
if [ "$2" == "reuse-all" ]
then
@@ -120,30 +119,32 @@ do
fi
# Run netmhcpan4
- OUT_DIR=predictions/${subset}.netmhcpan4
- REUSE1=""
- REUSE2=""
- if [ "$subset" == "all" ]
- then
- #REUSE1="predictions/chr1.netmhcpan4"
- # TODO: switch this back
- REUSE1="$EXISTING_DATA"/predictions/chr1.netmhcpan4
- fi
- if [ "${2:-reuse-none}" != "reuse-none" ]
- then
- REUSE2="$EXISTING_DATA"/$OUT_DIR
- fi
+ for kind in el ba
+ do
+ OUT_DIR=predictions/${subset}.netmhcpan4.$kind
+ REUSE1=""
+ REUSE2=""
+ if [ "$subset" == "all" ]
+ then
+ REUSE1="predictions/chr1.netmhcpan4.$kind"
+ fi
+ if [ "${2:-reuse-none}" != "reuse-none" ]
+ then
+ REUSE2="$EXISTING_DATA"/$OUT_DIR
+ fi
+
+ python run_predictors.py \
+ proteome_peptides.$subset.csv.bz2 \
+ --result-dtype "float16" \
+ --predictor netmhcpan4-$kind \
+ --chunk-size 10000 \
+ --allele $(cat alleles.txt) \
+ --out "$OUT_DIR" \
+ --worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
+ --cluster-script-prefix-path $SCRIPT_DIR/cluster_submit_script_header.mssm_hpc.nogpu.lsf \
+ --reuse-predictions "$REUSE1" "$REUSE2" $EXTRA_ARGS
+ done
- python run_predictors.py \
- proteome_peptides.$subset.csv.bz2 \
- --result-dtype "float16" \
- --predictor netmhcpan4 \
- --chunk-size 10000 \
- --allele $(cat alleles.txt) \
- --out "$OUT_DIR" \
- --worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
- --cluster-script-prefix-path $SCRIPT_DIR/cluster_submit_script_header.mssm_hpc.nogpu.lsf \
- --reuse-predictions "$REUSE1" "$REUSE2" $EXTRA_ARGS
# Run MHCflurry
for kind in with_mass_spec no_mass_spec
@@ -153,9 +154,7 @@ do
REUSE2=""
if [ "$subset" == "all" ]
then
- #REUSE1="predictions/chr1.mhcflurry.${kind}"
- # TODO: switch this back
- REUSE1="$EXISTING_DATA"/predictions/chr1.mhcflurry.${kind}
+ REUSE1="predictions/chr1.mhcflurry.${kind}"
fi
if [ "${2:-reuse-none}" != "reuse-none" ] && [ "${2:-reuse-none}" != "reuse-predictions-except-mhcflurry" ]
then
diff --git a/downloads-generation/data_mass_spec_benchmark/run_predictors.py b/downloads-generation/data_mass_spec_benchmark/run_predictors.py
index d4324737..be034ba9 100644
--- a/downloads-generation/data_mass_spec_benchmark/run_predictors.py
+++ b/downloads-generation/data_mass_spec_benchmark/run_predictors.py
@@ -43,7 +43,7 @@ parser.add_argument(
parser.add_argument(
"--predictor",
required=True,
- choices=("mhcflurry", "netmhcpan4"))
+ choices=("mhcflurry", "netmhcpan4-ba", "netmhcpan4-el"))
parser.add_argument(
"--mhcflurry-models-dir",
metavar="DIR",
@@ -88,7 +88,8 @@ add_cluster_parallelism_args(parser)
PREDICTOR_TO_COLS = {
"mhcflurry": ["affinity"],
- "netmhcpan4": ["affinity", "percentile_rank", "elution_score"],
+ "netmhcpan4-ba": ["affinity", "percentile_rank"],
+ "netmhcpan4-el": ["elution_score"],
}
@@ -376,9 +377,16 @@ def do_predictions_mhctools(work_item_dicts, constant_data=None):
result = {}
results.append((work_item_num, result))
- if predictor_name == "netmhcpan4":
+ if predictor_name == "netmhcpan4-ba":
predictor = mhctools.NetMHCpan4(
- alleles=alleles, program_name="netMHCpan-4.0")
+ alleles=alleles,
+ program_name="netMHCpan-4.0",
+ mode="binding_affinity")
+ elif predictor_name == "netmhcpan4-el":
+ predictor = mhctools.NetMHCpan4(
+ alleles=alleles,
+ program_name="netMHCpan-4.0",
+ mode="elution_score")
else:
raise ValueError("Unsupported", predictor_name)
--
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