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# 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<tag> "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(
'<species name="Homo sapiens (Human)" ncbiTaxID="9606"></species>',
text,
msg=f"Missing expected <species> 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)
|
