From 13adffc644560b66f763905bce7d45a0537878b7 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Tue, 1 Oct 2019 17:14:18 -0400
Subject: [PATCH] switch to chr1
---
.../GENERATE.WITH_HPC_CLUSTER.sh | 13 +++++++------
.../write_proteome_peptides.py | 11 +++++++++++
2 files changed, 18 insertions(+), 6 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 74de3546..d1fe18a9 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
@@ -35,9 +35,8 @@ REFERENCES_DIR=$(mhcflurry-downloads path data_references)
python write_proteome_peptides.py \
"$PEPTIDES" \
"${REFERENCES_DIR}/uniprot_proteins.csv.bz2" \
- --out proteome_peptides.csv
-ls -lh proteome_peptides.csv
-bzip2 proteome_peptides.csv
+ --chromosome 1 \
+ --out proteome_peptides.chr1.csv
python write_allele_list.py "$PEPTIDES" --out alleles.txt
@@ -46,12 +45,12 @@ mkdir predictions
for kind in with_mass_spec no_mass_spec
do
python run_mhcflurry.py \
- proteome_peptides.csv.bz2 \
- --chunk-size 1000000 \
+ proteome_peptides.chr1.csv \
+ --chunk-size 100000 \
--batch-size 65536 \
--models-dir "$(mhcflurry-downloads path models_class1_pan)/models.$kind" \
--allele $(cat alleles.txt) \
- --out "predictions/mhcflurry.$kind" \
+ --out "predictions/chr1.mhcflurry.$kind" \
--verbosity 1 \
--worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
--cluster-parallelism \
@@ -61,6 +60,8 @@ do
--cluster-script-prefix-path $SCRIPT_DIR/cluster_submit_script_header.mssm_hpc.lsf
done
+bzip2 proteome_peptides.chr1.csv
+
cp $SCRIPT_ABSOLUTE_PATH .
bzip2 LOG.txt
RESULT="$SCRATCH_DIR/${DOWNLOAD_NAME}.$(date +%Y%m%d).tar.bz2"
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 e18daf9e..29f9f728 100644
--- a/downloads-generation/data_mass_spec_benchmark/write_proteome_peptides.py
+++ b/downloads-generation/data_mass_spec_benchmark/write_proteome_peptides.py
@@ -27,6 +27,11 @@ parser.add_argument(
"--out",
metavar="OUT.csv",
help="Out file path")
+parser.add_argument(
+ "--chromosome",
+ metavar="CHR",
+ nargs="+",
+ help="Use only proteins from the specified chromosome(s)")
parser.add_argument(
"--debug-max-rows",
metavar="N",
@@ -62,6 +67,12 @@ def run():
df = df.loc[~df.protein_ensembl_primary.isnull()]
print("After: ", len(df))
+ if args.chromosome:
+ print("Subselecting to chromosome(s): ", *args.chromosome)
+ print("Before: ", len(df))
+ df = df.loc[df.protein_primary_ensembl_contig.isin(args.chromosome)]
+ print("After: ", len(df))
+
(flanking_length,) = list(
set(df.n_flank.str.len().unique()).union(
set(df.n_flank.str.len().unique())))
--
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