From f18d8d76cd617ca189f93f3e953603fdf1dd5efe Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Thu, 26 Dec 2019 10:06:35 -0500
Subject: [PATCH] fix
---
downloads-generation/data_curated/curate_ms_by_pmid.py | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/downloads-generation/data_curated/curate_ms_by_pmid.py b/downloads-generation/data_curated/curate_ms_by_pmid.py
index 46645ff6..a8f312dc 100755
--- a/downloads-generation/data_curated/curate_ms_by_pmid.py
+++ b/downloads-generation/data_curated/curate_ms_by_pmid.py
@@ -806,7 +806,10 @@ def handle_pmid_31844290(*filenames):
method='ffill')
sample_info = sample_info.loc[sample_info.index.isin(allele_table.index)]
sample_info = sample_info.loc[allele_table.index]
- sample_info["hla"] = [" ".join(row) for _, row in allele_table.iterrows()]
+ sample_info["hla"] = [
+ " ".join(row).replace("HLA-A*31:0102", "HLA-A*31:01") # fix a typo
+ for _, row in allele_table.iterrows()
+ ]
sample_info["sample_type"] = sample_info['Cancer type'].map({
'CLL': "B-CELL",
'GBM': "GLIOBLASTOMA_TISSUE",
--
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