From 15e69761d1a711da3a036c07efff82ac6eef7f71 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Tue, 31 Dec 2019 13:44:23 -0500
Subject: [PATCH] update allele_sequences download
---
downloads-generation/allele_sequences/GENERATE.sh | 5 ++++-
.../allele_sequences/select_alleles_to_disambiguate.py | 1 -
mhcflurry/downloads.yml | 2 +-
3 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/downloads-generation/allele_sequences/GENERATE.sh b/downloads-generation/allele_sequences/GENERATE.sh
index d320ed9a..8b9f4929 100755
--- a/downloads-generation/allele_sequences/GENERATE.sh
+++ b/downloads-generation/allele_sequences/GENERATE.sh
@@ -43,7 +43,10 @@ cp $SCRIPT_ABSOLUTE_PATH .
# pseudosequences but have associated training data
TRAINING_DATA="$(mhcflurry-downloads path data_curated)/curated_training_data.csv.bz2"
-python select_alleles_to_disambiguate.py "$TRAINING_DATA" --out training_data.alleles.txt
+python select_alleles_to_disambiguate.py \
+ "$TRAINING_DATA" \
+ --min-count 50 \
+ --out training_data.alleles.txt
# Human
wget -q ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/A_prot.fasta
diff --git a/downloads-generation/allele_sequences/select_alleles_to_disambiguate.py b/downloads-generation/allele_sequences/select_alleles_to_disambiguate.py
index 649df45b..cbee4a19 100644
--- a/downloads-generation/allele_sequences/select_alleles_to_disambiguate.py
+++ b/downloads-generation/allele_sequences/select_alleles_to_disambiguate.py
@@ -17,7 +17,6 @@ parser.add_argument(
parser.add_argument(
"--min-count",
type=int,
- default=50,
metavar="N",
help="Keep only alleles with at least N measurements")
parser.add_argument(
diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml
index 16a4d83e..940e0a40 100644
--- a/mhcflurry/downloads.yml
+++ b/mhcflurry/downloads.yml
@@ -74,7 +74,7 @@ releases:
default: false
- name: allele_sequences
- url: http://github.com/openvax/mhcflurry/releases/download/pan-dev1/allele_sequences.20190506.tar.bz2
+ url: https://github.com/openvax/mhcflurry/releases/download/1.4.0/allele_sequences.20191231.tar.bz2
default: false
- name: random_peptide_predictions
--
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