From 716e2251f338c30b4ce44ceab032882976721332 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 13 Dec 2019 12:40:52 -0500
Subject: [PATCH] test
---
.../models_class1_pan_refined/GENERATE.sh | 3 ++-
.../make_multiallelic_training_data.py | 23 ++++++++++++++++---
mhcflurry/downloads.yml | 2 +-
3 files changed, 23 insertions(+), 5 deletions(-)
diff --git a/downloads-generation/models_class1_pan_refined/GENERATE.sh b/downloads-generation/models_class1_pan_refined/GENERATE.sh
index a18b9389..17d63e6f 100755
--- a/downloads-generation/models_class1_pan_refined/GENERATE.sh
+++ b/downloads-generation/models_class1_pan_refined/GENERATE.sh
@@ -97,7 +97,8 @@ else
--hits "$(mhcflurry-downloads path data_mass_spec_annotated)/annotated_ms.csv.bz2" \
--expression "$(mhcflurry-downloads path data_curated)/rna_expression.csv.bz2" \
--decoys-per-hit 1 \
- --out train.multiallelic.csv
+ --out train.multiallelic.csv \
+ --alleles "HLA-A*02:01" "HLA-B*27:01" "HLA-C*07:01" "HLA-A*03:01" "HLA-B*15:01" "HLA-C*01:02"
fi
ALLELE_LIST=$(bzcat "$MONOALLELIC_TRAIN" | cut -f 1 -d , | grep -v allele | uniq | sort | uniq)
diff --git a/downloads-generation/models_class1_pan_refined/make_multiallelic_training_data.py b/downloads-generation/models_class1_pan_refined/make_multiallelic_training_data.py
index df14ce6f..998d8dd4 100644
--- a/downloads-generation/models_class1_pan_refined/make_multiallelic_training_data.py
+++ b/downloads-generation/models_class1_pan_refined/make_multiallelic_training_data.py
@@ -39,12 +39,17 @@ parser.add_argument(
metavar="CSV",
required=True,
help="File to write")
-
+parser.add_argument(
+ "--alleles",
+ nargs="+",
+ help="Include only the specified alleles")
def run():
args = parser.parse_args(sys.argv[1:])
hit_df = pandas.read_csv(args.hits)
expression_df = pandas.read_csv(args.expression, index_col=0).fillna(0)
+ hit_df["alleles"] = hit_df.hla.str.split()
+
hit_df = hit_df.loc[
(hit_df.mhc_class == "I") &
(hit_df.peptide.str.len() <= 15) &
@@ -64,8 +69,20 @@ def run():
"to",
len(new_hit_df))
hit_df = new_hit_df.copy()
-
- hit_df["alleles"] = hit_df.hla.str.split()
+ if args.alleles:
+ filter_alleles = set(args.alleles)
+ new_hit_df = hit_df.loc[
+ hit_df.alleles.isin.map(
+ lambda a: len(set(a).intersection(filter_alleles)) > 0)
+ ]
+ print(
+ "Selecting alleles",
+ args.alleles,
+ "reduced dataset from",
+ len(hit_df),
+ "to",
+ len(new_hit_df))
+ hit_df = new_hit_df.copy()
sample_table = hit_df.drop_duplicates("sample_id").set_index("sample_id")
grouped = hit_df.groupby("sample_id").nunique()
diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml
index 841372dc..1200b72e 100644
--- a/mhcflurry/downloads.yml
+++ b/mhcflurry/downloads.yml
@@ -30,7 +30,7 @@ releases:
default: false
- name: models_class1_pan_refined
- url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/models_class1_pan_refined.20191212b.tar.bz2
+ url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/models_class1_pan_refined.20191212c.tar.bz2
default: false
- name: models_class1_pan_variants
--
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