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Convert HGNC ids to their symbol (#1972)

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There are entries in some var indexes like HGNC:18790. We'd like to convert that to its symbol, NSG1.
This commit is contained in:
Marcus Kinsella
2020-11-06 09:27:49 -08:00
committed by GitHub
parent 39a1124c35
commit e892e64685
2 changed files with 8 additions and 0 deletions
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server/test/unit/converters/schema/test_gene_symbol.py
+5
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@@ -41,6 +41,11 @@ class TestHGNCSymbolChecker(unittest.TestCase):
self.assertEqual(self.hgnc_checker.upgrade_symbol("NOTASYMBOL"), "NOTASYMBOL")
self.assertEqual(self.hgnc_checker.upgrade_symbol("notasymbol"), "notasymbol")
# Upgrade HGNC ids unless you can't find it
self.assertEqual(self.hgnc_checker.upgrade_symbol("HGNC:286"), "ADRB2")
self.assertEqual(self.hgnc_checker.upgrade_symbol("HGNC:4812"), "HAP1")
self.assertEqual(self.hgnc_checker.upgrade_symbol("HGNC:123456"), "HGNC:123456")
def test_check_symbol(self):
self.assertEqual(self.hgnc_checker.check_symbol("SEPT1"), gene_symbol.SymbolStatus.UPGRADABLE)
self.assertEqual(self.hgnc_checker.check_symbol("DIFF6"), gene_symbol.SymbolStatus.AMBIGUOUS)