# 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. import unittest import sys from Bio import SeqIO from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio._py3k import StringIO test_files = { "dna": ["SeqXML/dna_example.xml", 4], "rna": ["SeqXML/rna_example.xml", 5], "protein": ["SeqXML/protein_example.xml", 5], "globalSpecies": ["SeqXML/global_species_example.xml", 2], } corrupt_files = [ "SeqXML/corrupt_example1.xml", "SeqXML/corrupt_example2.xml", ] def assert_equal_records(testCase, record_a, record_b): testCase.assertEqual(record_a.id, record_b.id) testCase.assertEqual(record_a.name, record_b.name) testCase.assertEqual(record_a.description, record_b.description) testCase.assertEqual(str(record_a.seq), str(record_b.seq)) testCase.assertEqual(record_a.dbxrefs, record_b.dbxrefs) testCase.assertEqual(record_a.annotations, record_a.annotations) class TestSimpleRead(unittest.TestCase): def test_check_SeqIO(self): """Files readable using parser via SeqIO.""" for key in test_files: records = list(SeqIO.parse(test_files[key][0], "seqxml")) self.assertEqual(len(records), test_files[key][1]) class TestDetailedRead(unittest.TestCase): records = {} def setUp(self): for key in test_files: self.records[key] = list(SeqIO.parse(test_files[key][0], "seqxml")) def test_special_characters_desc(self): """Read special XML characters in description.""" self.assertEqual(self.records["dna"][2].description, u'some special characters in the description\n "quoted string"') # TODO - Fix this failure under Windows with Python 3.1 and 3.2 if not (sys.platform == "win32" and sys.version_info[0] >= 3): def test_unicode_characters_desc(self): """Test special unicode characters in the description.""" self.assertEqual(self.records["rna"][2].description, u"\u00E5\u00C5\u00FC\u00F6\u00D6\u00DF\u00F8\u00E4\u00A2\u00A3$\u20AC\u9999\u80A0") def test_full_characters_set_read(self): """Read full characters set for each type""" self.assertEqual(str(self.records["dna"][1].seq), "ACGTMRWSYKVHDBXN.-") self.assertEqual(str(self.records["rna"][1].seq), "ACGUMRWSYKVHDBXN.-") self.assertEqual(str(self.records["protein"][1].seq), "ABCDEFGHIJKLMNOPQRSTUVWXYZ.-*") def test_duplicated_property(self): """Read property with multiple values""" self.assertEqual(self.records["protein"][2].annotations["test"], [u"1", u"2", u"3"]) def test_duplicated_dbxref(self): """Read multiple cross references to a single source""" self.assertEqual(self.records["protein"][2].dbxrefs, [u"someDB:G001", u"someDB:G002"]) def test_read_minimal_required(self): """Check minimal record.""" minimalRecord = SeqRecord(id="test", seq=Seq("abc")) minimalRecord.annotations["source"] = u"Ensembl" 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"], u"Uniprot") def test_empty_description(self): """Check empty description.""" self.assertEqual(self.records["rna"][4].description, SeqRecord(id="", seq=Seq("")).description) class TestReadAndWrite(unittest.TestCase): def test_read_write_rna(self): """Read and write RNA.""" read1_records = list(SeqIO.parse(test_files["rna"][0], "seqxml")) self._write_parse_and_compare(read1_records) def test_read_write_dna(self): """Read and write DNA.""" read1_records = list(SeqIO.parse(test_files["dna"][0], "seqxml")) self._write_parse_and_compare(read1_records) def test_read_write_protein(self): """Read and write protein.""" read1_records = list(SeqIO.parse(test_files["protein"][0], "seqxml")) self._write_parse_and_compare(read1_records) def test_read_write_globalSpecies(self): """Read and write global species.""" read1_records = list(SeqIO.parse(test_files["globalSpecies"][0], "seqxml")) self._write_parse_and_compare(read1_records) def _write_parse_and_compare(self, read1_records): handle = StringIO() 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): assert_equal_records(self, record1, record2) 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 = StringIO() SeqIO.write(record, handle, "seqxml") handle.seek(0) output = handle.getvalue() self.assertTrue("Homo sapiens (Human)" in output) self.assertTrue("9606" in output) if '' in output: # Good, but don't get this (do we?) pass elif '' in output: # Not as concise, but fine (seen on C Python) pass elif '' in output: # Jython uses a different order pass elif '' in output: # This would be fine too, but don't get this (do we?) pass else: raise ValueError("Mising expected tag: %r" % output) class TestReadCorruptFiles(unittest.TestCase): def test_for_errors(self): """Handling of corrupt files.""" for filename in corrupt_files: iterator = SeqIO.parse(filename, "seqxml") self.assertRaises(ValueError, next, iterator) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)