mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-03 02:18:12 +08:00
Marcus Kinsella
78176f9711
Add the `cellxgene schema apply` and `cellxgene schema validate` subcommands. The first takes an h5ad file and a yaml with config information and produces a new h5ad that follows the cellxgene data integration schema. The second takes an h5ad and checks if it follows the schema version written into its metadata. Both are currently marked as "experimental" as the primary intended users are still at CZI.
57 lines
2.7 KiB
Python
57 lines
2.7 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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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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