def testXMLInput(self):
"""
Test conversion of a chunk of BLAST XML. This is highly incomplete
in what it tests.
"""
mockOpener = mockOpen(read_data=RECORD)
with patch.object(builtins, 'open', mockOpener):
reader = XMLRecordsReader('file.xml')
record1, record2 = list(reader.records())
self.assertEqual(0, len(record1.alignments))
self.assertEqual(2, len(record2.alignments))
def testXMLInput(self):
"""
Test conversion of a chunk of BLAST XML. This is highly incomplete
in what it tests.
"""
mockOpener = mockOpen(read_data=RECORD)
with patch.object(builtins, 'open', mockOpener):
reader = XMLRecordsReader('file.xml')
record1, record2 = list(reader.records())
self.assertEqual(0, len(record1.alignments))
self.assertEqual(2, len(record2.alignments))
def testParams(self):
"""
When a BLAST XML file has been read, its parameters must be present
in the reader instance. We only test a subset of the parameters.
"""
mockOpener = mockOpen(read_data=RECORD)
with patch.object(builtins, 'open', mockOpener):
reader = XMLRecordsReader('file.xml')
list(reader.records())
self.assertEqual('BLASTN', reader.params['application'])
self.assertEqual('virus-nt-20130719', reader.params['database'])
def testParams(self):
"""
When a BLAST XML file has been read, its parameters must be present
in the reader instance. We only test a subset of the parameters.
"""
mockOpener = mockOpen(read_data=RECORD)
with patch.object(builtins, 'open', mockOpener):
reader = XMLRecordsReader('file.xml')
list(reader.records())
self.assertEqual('BLASTN', reader.params['application'])
self.assertEqual('virus-nt-20130719', reader.params['database'])