mirror of
https://github.com/chanzuckerberg/cellxgene.git
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Marcus Kinsella
e892e64685
There are entries in some var indexes like HGNC:18790. We'd like to convert that to its symbol, NSG1.
62 lines
3.0 KiB
Python
62 lines
3.0 KiB
Python
import os
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import unittest
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import pandas as pd
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from server.test import FIXTURES_ROOT
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from server.converters.schema import gene_symbol
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class TestHGNCSymbolChecker(unittest.TestCase):
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def setUp(self):
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self.test_hgnc_path = os.path.join(FIXTURES_ROOT, "hgnc_example.txt.gz")
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self.hgnc_checker = gene_symbol.HGNCSymbolChecker.from_hgnc_records(self.test_hgnc_path)
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def test_symbol_upgrade(self):
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self.assertEqual(self.hgnc_checker.upgrade_symbol("SEPT1"), "SEPTIN1")
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self.assertEqual(self.hgnc_checker.upgrade_symbol("ADRB2R"), "ADRB2")
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self.assertEqual(self.hgnc_checker.upgrade_symbol("BAR"), "ADRB2")
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self.assertEqual(self.hgnc_checker.upgrade_symbol("sept1"), "SEPTIN1")
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self.assertEqual(self.hgnc_checker.upgrade_symbol("AdRb2R"), "ADRB2")
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self.assertEqual(self.hgnc_checker.upgrade_symbol("bar"), "ADRB2")
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# Strip off seurat endings when appropriate
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self.assertEqual(self.hgnc_checker.upgrade_symbol("SEPT1.1"), "SEPTIN1")
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self.assertEqual(self.hgnc_checker.upgrade_symbol("ADRB2-1"), "ADRB2")
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# DIFF6 is ambiguous so don't upgrade it
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self.assertEqual(self.hgnc_checker.upgrade_symbol("DIFF6"), "DIFF6")
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self.assertEqual(self.hgnc_checker.upgrade_symbol("diff6"), "diff6")
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# ARG1 is approved
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self.assertEqual(self.hgnc_checker.upgrade_symbol("ARG1"), "ARG1")
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self.assertEqual(self.hgnc_checker.upgrade_symbol("arg1"), "ARG1")
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# HAP1 is both approved and withdrawn
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self.assertEqual(self.hgnc_checker.upgrade_symbol("HAP1"), "HAP1")
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self.assertEqual(self.hgnc_checker.upgrade_symbol("hap1"), "HAP1")
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# Leave unknown symbols alone
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self.assertEqual(self.hgnc_checker.upgrade_symbol("NOTASYMBOL"), "NOTASYMBOL")
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self.assertEqual(self.hgnc_checker.upgrade_symbol("notasymbol"), "notasymbol")
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# Upgrade HGNC ids unless you can't find it
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self.assertEqual(self.hgnc_checker.upgrade_symbol("HGNC:286"), "ADRB2")
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self.assertEqual(self.hgnc_checker.upgrade_symbol("HGNC:4812"), "HAP1")
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self.assertEqual(self.hgnc_checker.upgrade_symbol("HGNC:123456"), "HGNC:123456")
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def test_check_symbol(self):
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self.assertEqual(self.hgnc_checker.check_symbol("SEPT1"), gene_symbol.SymbolStatus.UPGRADABLE)
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self.assertEqual(self.hgnc_checker.check_symbol("DIFF6"), gene_symbol.SymbolStatus.AMBIGUOUS)
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self.assertEqual(self.hgnc_checker.check_symbol("NOTASYMBOL"), gene_symbol.SymbolStatus.UNKNOWN)
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# HAP1 is one of the approved and withdrawn symbols
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self.assertEqual(self.hgnc_checker.check_symbol("HAP1"), gene_symbol.SymbolStatus.APPROVED)
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def test_upgrade_index(self):
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index = pd.Index(["SEPT1", "DIFF6", "NOTASYMBOL", "bar", "SEPTIN1"])
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var_df = pd.DataFrame([[0] * len(index)], index=index)
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upgraded_index = gene_symbol.get_upgraded_var_index(var_df, hgnc_path=self.test_hgnc_path)
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self.assertEqual(upgraded_index.tolist(), ["SEPTIN1", "DIFF6", "NOTASYMBOL", "ADRB2", "SEPTIN1"])
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