# Copyright 2010 by Thomas Schmitt. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for SeqIO SeqXML module.""" import unittest from io import BytesIO from Bio import SeqIO from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord class TestSimpleRead(unittest.TestCase): def test_check_SeqIO(self): """Files readable using parser via SeqIO.""" records = list(SeqIO.parse("SeqXML/dna_example.xml", "seqxml")) self.assertEqual(len(records), 4) records = list(SeqIO.parse("SeqXML/rna_example.xml", "seqxml")) self.assertEqual(len(records), 5) records = list(SeqIO.parse("SeqXML/protein_example.xml", "seqxml")) self.assertEqual(len(records), 5) records = list(SeqIO.parse("SeqXML/global_species_example.xml", "seqxml")) self.assertEqual(len(records), 2) class TestDetailedRead(unittest.TestCase): records = {} def setUp(self): self.records["dna"] = list(SeqIO.parse("SeqXML/dna_example.xml", "seqxml")) self.records["rna"] = list(SeqIO.parse("SeqXML/rna_example.xml", "seqxml")) self.records["protein"] = list( SeqIO.parse("SeqXML/protein_example.xml", "seqxml") ) self.records["globalSpecies"] = list( SeqIO.parse("SeqXML/global_species_example.xml", "seqxml") ) def test_special_characters_desc(self): """Read special XML characters in description.""" self.assertEqual( self.records["dna"][2].description, 'some special characters in the description\n "quoted string"', ) def test_unicode_characters_desc(self): """Test special unicode characters in the description.""" self.assertEqual(self.records["rna"][2].description, "åÅüöÖßø䢣$€香肠") def test_full_characters_set_read(self): """Read full characters set for each type.""" self.assertEqual(self.records["dna"][1].seq, "ACGTMRWSYKVHDBXN.-") self.assertEqual(self.records["rna"][1].seq, "ACGUMRWSYKVHDBXN.-") self.assertEqual( self.records["protein"][1].seq, "ABCDEFGHIJKLMNOPQRSTUVWXYZ.-*" ) def test_duplicated_property(self): """Read property with multiple values.""" self.assertEqual( self.records["protein"][2].annotations["test"], ["1", "2", "3"] ) def test_duplicated_dbxref(self): """Read multiple cross references to a single source.""" self.assertEqual( self.records["protein"][2].dbxrefs, ["someDB:G001", "someDB:G002"] ) def test_read_minimal_required(self): """Check minimal record.""" minimalRecord = SeqRecord(id="test", seq=Seq("abc")) minimalRecord.annotations["source"] = "Ensembl" minimalRecord.annotations["molecule_type"] = "DNA" self.assertEqual(self.records["rna"][3].name, minimalRecord.name) self.assertEqual(self.records["dna"][3].annotations, minimalRecord.annotations) self.assertEqual(self.records["rna"][3].dbxrefs, minimalRecord.dbxrefs) self.assertEqual( self.records["protein"][3].description, minimalRecord.description ) def test_local_species(self): """Check local species.""" self.assertEqual(self.records["rna"][1].annotations["organism"], "Mus musculus") self.assertEqual(self.records["rna"][1].annotations["ncbi_taxid"], "10090") self.assertEqual( self.records["rna"][0].annotations["organism"], "Gallus gallus" ) self.assertEqual(self.records["rna"][0].annotations["ncbi_taxid"], "9031") def test_global_species(self): """Check global species.""" self.assertEqual( self.records["globalSpecies"][0].annotations["organism"], "Mus musculus" ) self.assertEqual( self.records["globalSpecies"][0].annotations["ncbi_taxid"], "10090" ) self.assertEqual( self.records["globalSpecies"][1].annotations["organism"], "Homo sapiens" ) self.assertEqual( self.records["globalSpecies"][1].annotations["ncbi_taxid"], "9606" ) def test_local_source_definition(self): """Check local source.""" self.assertEqual(self.records["protein"][4].annotations["source"], "Uniprot") def test_empty_description(self): """Check empty description.""" self.assertEqual( self.records["rna"][4].description, SeqRecord(id="", seq=Seq("")).description, ) class TestReadHeader(unittest.TestCase): def test_check_dna_header(self): """Check if the header information is parsed.""" records = SeqIO.parse("SeqXML/dna_example.xml", "seqxml") self.assertEqual(records.source, "Ensembl") self.assertEqual(records.sourceVersion, "56") self.assertEqual(records.seqXMLversion, "0.4") def test_check_rna_header(self): """Check if the header information is parsed.""" records = SeqIO.parse("SeqXML/rna_example.xml", "seqxml") self.assertEqual(records.source, "Ensembl") self.assertEqual(records.sourceVersion, "56") self.assertEqual(records.seqXMLversion, "0.3") def test_check_protein_header(self): """Check if the header information is parsed.""" records = SeqIO.parse("SeqXML/protein_example.xml", "seqxml") self.assertEqual(records.source, "Ensembl") self.assertEqual(records.sourceVersion, "56") self.assertEqual(records.seqXMLversion, "0.4") def test_check_global_species_example_header(self): """Check if the header information is parsed.""" records = SeqIO.parse("SeqXML/global_species_example.xml", "seqxml") self.assertEqual(records.speciesName, "Mus musculus") self.assertEqual(records.ncbiTaxID, "10090") self.assertEqual(records.source, "Ensembl") self.assertEqual(records.sourceVersion, "56") self.assertEqual(records.seqXMLversion, "0.4") class TestReadAndWrite(unittest.TestCase): def test_read_write_rna(self): """Read and write RNA.""" read1_records = list(SeqIO.parse("SeqXML/rna_example.xml", "seqxml")) self._write_parse_and_compare(read1_records) def test_read_write_dna(self): """Read and write DNA.""" read1_records = list(SeqIO.parse("SeqXML/dna_example.xml", "seqxml")) self._write_parse_and_compare(read1_records) def test_read_write_protein(self): """Read and write protein.""" read1_records = list(SeqIO.parse("SeqXML/protein_example.xml", "seqxml")) self._write_parse_and_compare(read1_records) def test_read_write_globalSpecies(self): """Read and write global species.""" read1_records = list(SeqIO.parse("SeqXML/global_species_example.xml", "seqxml")) self._write_parse_and_compare(read1_records) def _write_parse_and_compare(self, read1_records): handle = BytesIO() SeqIO.write(read1_records, handle, "seqxml") handle.seek(0) read2_records = list(SeqIO.parse(handle, "seqxml")) self.assertEqual(len(read1_records), len(read2_records)) for record1, record2 in zip(read1_records, read2_records): self.assertEqual(record1.id, record2.id) self.assertEqual(record1.name, record2.name) self.assertEqual(record1.description, record2.description) self.assertEqual(record1.seq, record2.seq) self.assertEqual(record1.dbxrefs, record2.dbxrefs) self.assertEqual(record1.annotations, record2.annotations) def test_write_species(self): """Test writing species from annotation tags.""" record = SeqIO.read("SwissProt/sp016", "swiss") self.assertEqual(record.annotations["organism"], "Homo sapiens (Human)") self.assertEqual(record.annotations["ncbi_taxid"], ["9606"]) handle = BytesIO() SeqIO.write(record, handle, "seqxml") handle.seek(0) output = handle.getvalue() text = output.decode("UTF-8") self.assertIn("Homo sapiens (Human)", text) self.assertIn("9606", text) self.assertIn( '', text, msg=f"Missing expected tag: {text!r}", ) class TestReadCorruptFiles(unittest.TestCase): def test_for_errors(self): """Handling of corrupt files.""" # SeqIO.parse reads the file in blocks until it finds the seqXML # element with global information such as the source and sourceVersion. # Since one block is likely large enough to cover the first few # entries in the file, the ValueError may be raised after we call # SeqIO.parse, before we start iterating over the file. def f(path): records = SeqIO.parse(path, "seqxml") for record in records: pass self.assertRaises(ValueError, f, "SeqXML/corrupt_example1.xml") self.assertRaises(ValueError, f, "SeqXML/corrupt_example2.xml") self.assertRaises(ValueError, f, "SeqXML/corrupt_example3.xml") class TestOldVersions(unittest.TestCase): def test_version01(self): """Test for version 0.1 specific features.""" records = list(SeqIO.parse("SeqXML/version_01_example.xml", "seqxml")) self.assertEqual(records[0].seq, "AAAAAACGTAAA") self.assertEqual(records[0].dbxrefs[0], "db:1") self.assertEqual(records[1].seq, "AAAUUUUCTGAA") self.assertEqual(records[2].seq, "GAKKVFIEDVSKEFVEEFIWPAVQSSALYE") def test_wrong_version(self): """Handling of wrong versions.""" def f(path): records = SeqIO.parse(path, "seqxml") for record in records: pass self.assertRaises(ValueError, f, "SeqXML/wrong_version1.xml") self.assertRaises(ValueError, f, "SeqXML/wrong_version2.xml") self.assertRaises(ValueError, f, "SeqXML/wrong_version3.xml") if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)