def testPopulationByInMemorySubjects(self):
"""
Passing a subjects keyword must result in the subjects being added
to the returned database.
"""
subjects = Reads()
subject1 = AARead('id1', 'FFF')
subject2 = AARead('id2', 'RRR')
subjects.add(subject1)
subjects.add(subject2)
db = DatabaseSpecifier().getDatabaseFromKeywords(subjects=subjects)
allSubjects = [subject.read for subject in db.getSubjects()]
self.assertEqual({subject1, subject2}, set(allSubjects))
def testPopulationFromFastaFile(self):
"""
Passing a databaseFasta keyword must result in the subjects in the
file being added to the returned database.
"""
data = '\n'.join(['>id1', 'FFF', '>id2', 'RRR'])
mockOpener = mockOpen(read_data=data)
with patch.object(builtins, 'open', mockOpener):
db = DatabaseSpecifier().getDatabaseFromKeywords(
databaseFasta='file.fasta')
allSubjects = [subject.read for subject in db.getSubjects()]
self.assertEqual(
{AARead('id1', 'FFF'), AARead('id2', 'RRR')}, set(allSubjects))
def testInMemoryDatabaseIsPopulated(self):
"""
Passing a database keyword with an in-memory database results in that
database being populated.
"""
original = Database()
subjects = Reads()
subject1 = AARead('id1', 'FFF')
subject2 = AARead('id2', 'RRR')
subjects.add(subject1)
subjects.add(subject2)
db = DatabaseSpecifier().getDatabaseFromKeywords(database=original,
subjects=subjects)
allSubjects = [subject.read for subject in db.getSubjects()]
self.assertEqual({subject1, subject2}, set(allSubjects))
def testPopulationFromInMemoryAndFastaFile(self):
"""
Passing both subjects and databaseFasta keywords must result in
all the subjects in memory and in the file being added to the returned
database.
"""
subjects = Reads()
subject1 = AARead('id1', 'FFF')
subject2 = AARead('id2', 'RRR')
subjects.add(subject1)
subjects.add(subject2)
data = '\n'.join(['>id3', 'FFFF', '>id4', 'RRRR'])
mockOpener = mockOpen(read_data=data)
with patch.object(builtins, 'open', mockOpener):
db = DatabaseSpecifier().getDatabaseFromKeywords(
subjects=subjects, databaseFasta='file.fasta')
allSubjects = [subject.read for subject in db.getSubjects()]
self.assertEqual(
{subject1, subject2,
AARead('id3', 'FFFF'),
AARead('id4', 'RRRR')}, set(allSubjects))