def test_getOrganism(self):
"""
Test that the Sequence object returns correctly the organism value.
"""
print 'Running %s ...' % getName()
s1 = self.sequenceListingFixture.create_sequence_instance(self.sequenceListing)
self.assertEqual('H**o sapiens', s1.getOrganism())
s2 = Sequence.objects.create(
sequenceListing = self.sequenceListing,
moltype = 'AA',
residues = 'MRTAVTAD')
self.assertEqual(None, s2.getOrganism())
views.feature_source_helper(s2, 'Drosophila melanogaster')
self.assertEqual('Drosophila melanogaster', s2.getOrganism())
s3 = Sequence.objects.create(
sequenceListing = self.sequenceListing,
moltype = 'RNA',
residues = 'caucaucaucaucaucau')
views.feature_source_helper(s3, 'Mus musculus')
self.assertEqual('Mus musculus', s3.getOrganism())
def create_custom_sequence_instance(self, sl, mt, res, org):
seq = Sequence.objects.create(
sequenceListing = sl,
moltype = mt,
residues = res)
views.feature_source_helper(seq, org)
return seq
def create_sequence_instance(self, sl):
seq = Sequence.objects.create(
sequenceListing = sl,
moltype = 'DNA',
residues = 'catcatcatcatcatcat')
views.feature_source_helper(seq, 'H**o sapiens')
return seq
def create_sequence_instance(self, sl):
currentSeqIdNo = len(sl.sequence_set.all()) + 1
currentSequenceName = 'test_seq_%i' % currentSeqIdNo
seq = Sequence.objects.create(sequenceListing=sl,
sequenceName=currentSequenceName,
moltype='DNA',
residues='catcatcatcatcatcat')
views.feature_source_helper(seq, 'H**o sapiens', 'genomic DNA')
return seq
def create_custom_sequence_instance(self, sl, mt, res, org, mtq):
currentSeqIdNo = len(sl.sequence_set.all()) + 1
currentSequenceName = 'test_seq_%i' % currentSeqIdNo
seq = Sequence.objects.create(sequenceListing=sl,
sequenceName=currentSequenceName,
moltype=mt,
residues=res)
views.feature_source_helper(seq, org, mtq)
return seq
def test_getOrganism(self):
"""
Test that the Sequence object returns correctly the organism value.
"""
print 'Running %s ...' % getName()
s1 = self.sequenceListingFixture.create_sequence_instance(
self.sequenceListing)
self.assertEqual('H**o sapiens', s1.getOrganism())
s2 = Sequence.objects.create(sequenceListing=self.sequenceListing,
moltype='AA',
residues='MRTAVTAD')
self.assertEqual(None, s2.getOrganism())
views.feature_source_helper(s2, 'Drosophila melanogaster', 'protein')
self.assertEqual('Drosophila melanogaster', s2.getOrganism())
s3 = Sequence.objects.create(sequenceListing=self.sequenceListing,
moltype='RNA',
residues='caucaucaucaucaucau')
views.feature_source_helper(s3, 'Mus musculus', 'genomic RNA')
self.assertEqual('Mus musculus', s3.getOrganism())