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Commit f18d8d76 authored by Tim O'Donnell's avatar Tim O'Donnell
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fix

parent 01085863
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......@@ -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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