From 15b85d7c23b095f213a69588451ee5784716bb67 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 27 Sep 2019 14:38:56 -0400
Subject: [PATCH] fix
---
downloads-generation/data_curated/GENERATE.sh | 5 ++++-
downloads-generation/data_curated/curate_by_pmid.py | 10 ++++++++++
mhcflurry/downloads.yml | 2 +-
3 files changed, 15 insertions(+), 2 deletions(-)
diff --git a/downloads-generation/data_curated/GENERATE.sh b/downloads-generation/data_curated/GENERATE.sh
index 6e88bc7f..fd041f93 100755
--- a/downloads-generation/data_curated/GENERATE.sh
+++ b/downloads-generation/data_curated/GENERATE.sh
@@ -40,7 +40,10 @@ do
CURATE_BY_PMID_ARGS+=$(echo --item $pmid raw/$pmid/* ' ')
done
-time python curate_by_pmid.py $CURATE_BY_PMID_ARGS --out curated.by_pmid.csv --debug
+time python curate_by_pmid.py $CURATE_BY_PMID_ARGS \
+ --out nontraining_curated.by_pmid.csv
+
+bzip2 nontraining_curated.by_pmid.csv
rm -rf raw
diff --git a/downloads-generation/data_curated/curate_by_pmid.py b/downloads-generation/data_curated/curate_by_pmid.py
index 5d62f62b..4f1950e5 100755
--- a/downloads-generation/data_curated/curate_by_pmid.py
+++ b/downloads-generation/data_curated/curate_by_pmid.py
@@ -126,6 +126,12 @@ def handle_pmid_23481700(filename):
results.append(result_df)
result_df = pandas.concat(results, ignore_index=True)
+
+ # Rename samples to avoid a collision with the JY sample in PMID 25576301.
+ result_df.sample_id = result_df.sample_id.map({
+ "JY": "JY.2015",
+ "HHC": "HHC.2015",
+ })
return result_df
@@ -666,6 +672,10 @@ def run():
else:
print("No nulls.")
+ # Each sample should be coming from only one experiment.
+ assert df.groupby("sample_id").pmid.nunique().max() == 1, (
+ df.groupby("sample_id").pmid.nunique().sort_values())
+
df.to_csv(args.out, index=False)
print("Wrote: %s" % os.path.abspath(args.out))
diff --git a/mhcflurry/downloads.yml b/mhcflurry/downloads.yml
index fe5e6f28..3e05c91e 100644
--- a/mhcflurry/downloads.yml
+++ b/mhcflurry/downloads.yml
@@ -50,7 +50,7 @@ releases:
default: false
- name: data_curated
- url: https://github.com/openvax/mhcflurry/releases/download/pre-1.4.0/data_curated.20190925.tar.bz2
+ url: https://github.com/openvax/mhcflurry/releases/download/pre-1.4.0/data_curated.20190927.tar.bz2
default: true
# Older downloads
--
GitLab