def setUp(self):
self.test_indices1 = [3734, 4034]
self.extra_indices = [[4092, 4332], [4399, 5185], [5249, 6565],
[6630, 7436]]
test_identifier1 = 8
self.extra_identifiers = [9, 10, 11, 12]
self.test_phase1 = 0
self.extra_phases = [2, 1, 0, 0]
test_parent_id1 = 2
self.test_cds0 = CDS(identifier=test_identifier1,
indices=self.test_indices1,
score=None,
phase=self.test_phase1,
strand='-',
parent_id=test_parent_id1)
self.test_cds1 = CDS(identifier=test_identifier1,
indices=self.test_indices1,
score=None,
phase=self.test_phase1,
strand='+',
parent_id=test_parent_id1)
for ind_pair in self.extra_indices:
self.test_cds1.add_indices(ind_pair)
for ident in self.extra_identifiers:
self.test_cds1.add_identifier(ident)
for phase in self.extra_phases:
self.test_cds1.add_phase(phase)
def test_sort_attributes(self):
cds = CDS()
cds.indices = [[25, 30], [5, 10]] # out of order!
cds.identifier = ["cds2", "cds1"]
cds.phase = [1, 0]
self.assertEquals("cds1", cds.identifier[1])
self.assertEquals([25, 30], cds.indices[0])
self.assertEquals(1, cds.phase[0])
cds.sort_attributes()
self.assertEquals("cds1", cds.identifier[0])
self.assertEquals([5, 10], cds.indices[0])
self.assertEquals(0, cds.phase[0])
def process_cds_line(self, line):
"""Extracts arguments from a line and adds them to a CDS, or makes a new one."""
kwargs = self.extract_cds_args(line)
if not kwargs:
return
parent_id = kwargs['parent_id']
if parent_id not in self.mrnas:
self.orphans.append(line)
return
parent_mrna = self.mrnas[parent_id]
if parent_mrna.cds:
self.update_cds(line, parent_mrna.cds)
else:
parent_mrna.cds = CDS(**kwargs)
def test_to_gff(self):
expected1 = "sctg_0080_0020\tmaker\tCDS\t3734\t4034\t.\t+\t0\tID=8;Parent=2;foo=dog\n"
expected2 = "sctg_0080_0020\tmaker\tCDS\t4092\t4332\t.\t+\t2\tID=9;Parent=2;foo=dog\n"
expected3 = "sctg_0080_0020\tmaker\tCDS\t4399\t5185\t.\t+\t1\tID=10;Parent=2;foo=dog\n"
expected4 = "sctg_0080_0020\tmaker\tCDS\t5249\t6565\t.\t+\t0\tID=11;Parent=2;foo=dog\n"
expected5 = "sctg_0080_0020\tmaker\tCDS\t6630\t7436\t.\t+\t0\tID=12;Parent=2;foo=dog\n"
expected = expected1 + expected2 + expected3 + expected4 + expected5
self.test_cds1.add_annotation(
'foo', 'dog') # Make sure our annotations are working
actual = self.test_cds1.to_gff(seq_name="sctg_0080_0020",
source="maker")
self.assertEquals(expected, actual)
# what if identifier, parent_id are strings? does it matter?
test_cds2 = CDS(identifier='foo1',
indices=self.test_indices1,
score=None,
strand='+',
phase=self.test_phase1,
parent_id='bar7')
extra_identifiers2 = ['foo2', 'foo3', 'foo4', 'foo5']
for ind_pair in self.extra_indices:
test_cds2.add_indices(ind_pair)
for ident in extra_identifiers2:
test_cds2.add_identifier(ident)
for phase in self.extra_phases:
test_cds2.add_phase(phase)
expected1 = "sctg_0080_0020\tmaker\tCDS\t3734\t4034\t.\t+\t0\tID=foo1;Parent=bar7\n"
expected2 = "sctg_0080_0020\tmaker\tCDS\t4092\t4332\t.\t+\t2\tID=foo2;Parent=bar7\n"
expected3 = "sctg_0080_0020\tmaker\tCDS\t4399\t5185\t.\t+\t1\tID=foo3;Parent=bar7\n"
expected4 = "sctg_0080_0020\tmaker\tCDS\t5249\t6565\t.\t+\t0\tID=foo4;Parent=bar7\n"
expected5 = "sctg_0080_0020\tmaker\tCDS\t6630\t7436\t.\t+\t0\tID=foo5;Parent=bar7\n"
expected = expected1 + expected2 + expected3 + expected4 + expected5
actual = test_cds2.to_gff(seq_name="sctg_0080_0020", source="maker")
self.assertEquals(expected, actual)
expected1 = "sctg_0080_0020\tmaker\tCDS\t3734\t4034\t.\t+\t0\tID=foo1;Parent=bar7\n"
expected2 = "sctg_0080_0020\tmaker\tCDS\t4092\t4332\t.\t+\t2\tID=foo2;Parent=bar7\n"
expected3 = "sctg_0080_0020\tmaker\tCDS\t4399\t5185\t.\t+\t1\tID=foo3;Parent=bar7\n"
expected4 = "sctg_0080_0020\tmaker\tCDS\t5249\t6565\t.\t+\t0\tID=foo4;Parent=bar7\n"
expected5 = "sctg_0080_0020\tmaker\tCDS\t6630\t7436\t.\t+\t0\tID=foo5;Parent=bar7\n"
expected = expected1 + expected2 + expected3 + expected4 + expected5
actual = test_cds2.to_gff(seq_name="sctg_0080_0020", source="maker")
self.assertEquals(expected, actual)
def test_cds_constructor(self):
self.assertEquals('CDS', self.test_cds0.__class__.__name__)
# should also be able to construct w/o all the params...
empty_cds = CDS()
self.assertEquals('CDS', empty_cds.feature_type)
