From dd770b243061f9f19fc2774f805fc90f1d1a68f1 Mon Sep 17 00:00:00 2001
From: Timothy ODonnell <odonnt02@li03c03.chimera.hpc.mssm.edu>
Date: Mon, 30 Sep 2019 21:56:45 -0400
Subject: [PATCH] fix
---
.../GENERATE.WITH_HPC_CLUSTER.sh | 18 ++++++++----------
.../data_mass_spec_benchmark/run_mhcflurry.py | 2 +-
.../write_proteome_peptides.py | 2 --
3 files changed, 9 insertions(+), 13 deletions(-)
diff --git a/downloads-generation/data_mass_spec_benchmark/GENERATE.WITH_HPC_CLUSTER.sh b/downloads-generation/data_mass_spec_benchmark/GENERATE.WITH_HPC_CLUSTER.sh
index 132d78d3..bfcb1d14 100755
--- a/downloads-generation/data_mass_spec_benchmark/GENERATE.WITH_HPC_CLUSTER.sh
+++ b/downloads-generation/data_mass_spec_benchmark/GENERATE.WITH_HPC_CLUSTER.sh
@@ -15,8 +15,8 @@ rm -rf "$SCRATCH_DIR/$DOWNLOAD_NAME"
mkdir "$SCRATCH_DIR/$DOWNLOAD_NAME"
# Send stdout and stderr to a logfile included with the archive.
-#exec > >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt")
-#exec 2> >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt" >&2)
+exec > >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt")
+exec 2> >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt" >&2)
# Log some environment info
date
@@ -29,17 +29,15 @@ cp $SCRIPT_DIR/write_proteome_peptides.py .
cp $SCRIPT_DIR/run_mhcflurry.py .
cp $SCRIPT_DIR/write_allele_list.py .
-
PEPTIDES=$(mhcflurry-downloads path data_mass_spec_annotated)/annotated_ms.csv.bz2
REFERENCES_DIR=$(mhcflurry-downloads path data_references)
-#python write_proteome_peptides.py \
-# "$PEPTIDES" \
-# "${REFERENCES_DIR}/uniprot_proteins.csv.bz2" \
-# --out proteome_peptides.csv
-#ls -lh proteome_peptides.csv
-#bzip2 proteome_peptides.csv
-ln -s ~/Dropbox/sinai/projects/201808-mhcflurry-pan/20190622-models/proteome_peptides.csv.bz2 proteome_peptides.csv.bz2
+python write_proteome_peptides.py \
+ "$PEPTIDES" \
+ "${REFERENCES_DIR}/uniprot_proteins.csv.bz2" \
+ --out proteome_peptides.csv
+ls -lh proteome_peptides.csv
+bzip2 proteome_peptides.csv
python write_allele_list.py "$PEPTIDES" --out alleles.txt
diff --git a/downloads-generation/data_mass_spec_benchmark/run_mhcflurry.py b/downloads-generation/data_mass_spec_benchmark/run_mhcflurry.py
index 435a6046..84fb4fe5 100644
--- a/downloads-generation/data_mass_spec_benchmark/run_mhcflurry.py
+++ b/downloads-generation/data_mass_spec_benchmark/run_mhcflurry.py
@@ -55,7 +55,7 @@ parser.add_argument(
parser.add_argument(
"--chunk-size",
type=int,
- default=1000000,
+ default=100000000,
help="Num peptides per job. Default: %(default)s")
parser.add_argument(
"--batch-size",
diff --git a/downloads-generation/data_mass_spec_benchmark/write_proteome_peptides.py b/downloads-generation/data_mass_spec_benchmark/write_proteome_peptides.py
index bc9c7228..e18daf9e 100644
--- a/downloads-generation/data_mass_spec_benchmark/write_proteome_peptides.py
+++ b/downloads-generation/data_mass_spec_benchmark/write_proteome_peptides.py
@@ -12,8 +12,6 @@ import pandas
import tqdm # progress bar
tqdm.monitor_interval = 0 # see https://github.com/tqdm/tqdm/issues/481
-import shellinford
-
parser = argparse.ArgumentParser(usage=__doc__)
--
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