def test_constructor(self):
self.gp1 = GenePart()
self.assertEquals(0, len(self.gp1.indices))
self.assertFalse(self.gp1.score)
self.assertFalse(self.gp1.parent_id)
self.assertEquals('CDS', self.gp2.feature_type)
self.assertEquals('+', self.gp1.strand)
def setUp(self):
self.gp1 = GenePart()
self.gp2 = GenePart(feature_type='CDS', indices=[1, 44])
self.gp2.add_indices([65, 103])
self.gp2.identifier = ['foo1', 'foo2']
self.gp2.parent_id = 'mama'
self.gp3 = GenePart(feature_type='exon')
def add_stop_codon(self, indices):
"""Adds a stop_codon GenePart to MRNA.other_features"""
stop_id = self.identifier + ":stop"
stop_parent_id = self.identifier
stop = GenePart(feature_type='stop_codon', identifier=stop_id, \
indices=indices, parent_id=stop_parent_id, strand=self.strand)
self.add_other_feature(stop)
def test_constructor(self):
self.gp1 = GenePart()
self.assertEquals(0, len(self.gp1.indices))
self.assertFalse(self.gp1.score)
self.assertFalse(self.gp1.parent_id)
self.assertEquals('CDS', self.gp2.feature_type)
self.assertEquals('+', self.gp1.strand)
def add_start_codon(self, indices):
"""Adds a start_codon GenePart to MRNA.other_features"""
# TODO figure out naming scheme...
start_id = self.identifier + ":start"
start_parent_id = self.identifier
start = GenePart(feature_type='start_codon', identifier=start_id, \
indices=indices, parent_id=start_parent_id, strand=self.strand)
self.add_other_feature(start)
def process_other_feature_line(self, line):
"""Extracts arguments from a line and instantiates a GenePart from them."""
kwargs = self.extract_other_feature_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]
parent_mrna.other_features.append(GenePart(**kwargs))
def test_sort_attributes(self):
gp = GenePart()
gp.indices = [[25, 30], [5, 10]] # out of order!
gp.identifier = ["gp2", "gp1"]
gp.score = [10, 8]
self.assertEquals("gp1", gp.identifier[1])
self.assertEquals([25, 30], gp.indices[0])
gp.sort_attributes()
self.assertEquals("gp1", gp.identifier[0])
self.assertEquals([5, 10], gp.indices[0])
def setUp(self):
self.gp1 = GenePart()
self.gp2 = GenePart(feature_type='CDS', indices=[1, 44])
self.gp2.add_indices([65, 103])
self.gp2.identifier = ['foo1', 'foo2']
self.gp2.parent_id = 'mama'
self.gp3 = GenePart(feature_type='exon')
def test_sort_attributes(self):
gp = GenePart()
gp.indices = [[25, 30], [5, 10]] # out of order!
gp.identifier = ["gp2", "gp1"]
gp.score = [10, 8]
self.assertEquals("gp1", gp.identifier[1])
self.assertEquals([25, 30], gp.indices[0])
gp.sort_attributes()
self.assertEquals("gp1", gp.identifier[0])
self.assertEquals([5, 10], gp.indices[0])
class TestGenePart(unittest.TestCase):
def setUp(self):
self.gp1 = GenePart()
self.gp2 = GenePart(feature_type='CDS', indices=[1, 44])
self.gp2.add_indices([65, 103])
self.gp2.identifier = ['foo1', 'foo2']
self.gp2.parent_id = 'mama'
self.gp3 = GenePart(feature_type='exon')
def test_constructor(self):
self.gp1 = GenePart()
self.assertEquals(0, len(self.gp1.indices))
self.assertFalse(self.gp1.score)
self.assertFalse(self.gp1.parent_id)
self.assertEquals('CDS', self.gp2.feature_type)
self.assertEquals('+', self.gp1.strand)
def test_add_indices(self):
self.assertEquals(2, len(self.gp2.indices))
self.gp2.add_indices([150, 197])
self.assertEquals(3, len(self.gp2.indices))
self.assertEquals(0, len(self.gp3.indices))
self.gp3.add_indices([77, 144])
self.assertEquals(1, len(self.gp3.indices))
# error check
self.assertRaises(ValueError, self.gp3.add_indices, 7)
self.assertRaises(ValueError, self.gp3.add_indices, 'foo')
def test_add_identifier(self):
self.assertEquals(0, len(self.gp3.identifier))
self.gp3.add_identifier('7')
self.assertEquals(1, len(self.gp3.identifier))
def test_add_annotation(self):
gp = GenePart()
self.assertFalse(gp.annotations)
gp.add_annotation("gag_flag", "this gene part rulz")
self.assertTrue(gp.annotations)
def test_gagflagged(self):
gp = GenePart()
self.assertFalse(gp.gagflagged())
gp.add_annotation("gag_flag", "awesome flag")
self.assertTrue(gp.gagflagged())
def test_length(self):
self.assertEquals(83, self.gp2.length())
# what if no indices at all?
self.assertFalse(self.gp1.length())
def test_adjust_indices(self):
self.gp2.adjust_indices(10)
self.assertEquals(54, self.gp2.indices[0][1])
# now put it back
self.gp2.adjust_indices(-10)
self.assertEquals(65, self.gp2.indices[1][0])
def test_adjust_indices_after_start_index(self):
self.gp2.adjust_indices(10, 50)
self.assertEqual(44, self.gp2.indices[0][1])
self.assertEqual(75, self.gp2.indices[1][0])
def test_generate_attribute_entry(self):
# test .generate_attribute_entry
expected = "ID=foo1;Parent=mama\n"
self.assertEquals(expected, self.gp2.generate_attribute_entry(0))
expected = "ID=foo2;Parent=mama\n"
self.assertEquals(expected, self.gp2.generate_attribute_entry(1))
# what if index out of range?
self.assertFalse(self.gp2.generate_attribute_entry(2))
# what if no identifier or parent_id?
self.assertFalse(self.gp1.generate_attribute_entry(0))
self.gp1.parent_id = 'dad'
self.assertFalse(self.gp1.generate_attribute_entry(0))
def test_str(self):
expected = "CDS (first ID=foo1)"
self.assertEquals(expected, str(self.gp2))
def test_to_gff(self):
# test .to_gff
seq_name = "sctg_0001_0001"
source = 'maker'
strand = '+'
expected = "sctg_0001_0001\tmaker\tCDS\t1\t44\t.\t+\t.\t"
expected += "ID=foo1;Parent=mama\n"
expected += "sctg_0001_0001\tmaker\tCDS\t65\t103\t.\t+\t.\t"
expected += "ID=foo2;Parent=mama\n"
actual = self.gp2.to_gff(seq_name=seq_name, source=source)
self.assertEquals(expected, actual)
# what if no indices, etc.?
self.assertFalse(self.gp1.to_gff(seq_name="foo", source="bar"))
def test_gagflagged(self):
gp = GenePart()
self.assertFalse(gp.gagflagged())
gp.add_annotation("gag_flag", "awesome flag")
self.assertTrue(gp.gagflagged())
def test_add_annotation(self):
gp = GenePart()
self.assertFalse(gp.annotations)
gp.add_annotation("gag_flag", "this gene part rulz")
self.assertTrue(gp.annotations)
class TestGenePart(unittest.TestCase):
def setUp(self):
self.gp1 = GenePart()
self.gp2 = GenePart(feature_type='CDS', indices=[1, 44])
self.gp2.add_indices([65, 103])
self.gp2.identifier = ['foo1', 'foo2']
self.gp2.parent_id = 'mama'
self.gp3 = GenePart(feature_type='exon')
def test_constructor(self):
self.gp1 = GenePart()
self.assertEquals(0, len(self.gp1.indices))
self.assertFalse(self.gp1.score)
self.assertFalse(self.gp1.parent_id)
self.assertEquals('CDS', self.gp2.feature_type)
self.assertEquals('+', self.gp1.strand)
def test_add_indices(self):
self.assertEquals(2, len(self.gp2.indices))
self.gp2.add_indices([150, 197])
self.assertEquals(3, len(self.gp2.indices))
self.assertEquals(0, len(self.gp3.indices))
self.gp3.add_indices([77, 144])
self.assertEquals(1, len(self.gp3.indices))
# error check
self.assertRaises(ValueError, self.gp3.add_indices, 7)
self.assertRaises(ValueError, self.gp3.add_indices, 'foo')
def test_add_identifier(self):
self.assertEquals(0, len(self.gp3.identifier))
self.gp3.add_identifier('7')
self.assertEquals(1, len(self.gp3.identifier))
def test_add_annotation(self):
gp = GenePart()
self.assertFalse(gp.annotations)
gp.add_annotation("gag_flag", "this gene part rulz")
self.assertTrue(gp.annotations)
def test_sort_attributes(self):
gp = GenePart()
gp.indices = [[25, 30], [5, 10]] # out of order!
gp.identifier = ["gp2", "gp1"]
gp.score = [10, 8]
self.assertEquals("gp1", gp.identifier[1])
self.assertEquals([25, 30], gp.indices[0])
gp.sort_attributes()
self.assertEquals("gp1", gp.identifier[0])
self.assertEquals([5, 10], gp.indices[0])
def test_gagflagged(self):
gp = GenePart()
self.assertFalse(gp.gagflagged())
gp.add_annotation("gag_flag", "awesome flag")
self.assertTrue(gp.gagflagged())
def test_length(self):
self.assertEquals(83, self.gp2.length())
# what if no indices at all?
self.assertFalse(self.gp1.length())
def test_adjust_indices(self):
self.gp2.adjust_indices(10)
self.assertEquals(54, self.gp2.indices[0][1])
# now put it back
self.gp2.adjust_indices(-10)
self.assertEquals(65, self.gp2.indices[1][0])
def test_adjust_indices_after_start_index(self):
self.gp2.adjust_indices(10, 50)
self.assertEqual(44, self.gp2.indices[0][1])
self.assertEqual(75, self.gp2.indices[1][0])
def test_generate_attribute_entry(self):
# test .generate_attribute_entry
expected = "ID=foo1;Parent=mama\n"
self.assertEquals(expected, self.gp2.generate_attribute_entry(0))
expected = "ID=foo2;Parent=mama\n"
self.assertEquals(expected, self.gp2.generate_attribute_entry(1))
# what if index out of range?
self.assertFalse(self.gp2.generate_attribute_entry(2))
# what if no identifier or parent_id?
self.assertFalse(self.gp1.generate_attribute_entry(0))
self.gp1.parent_id = 'dad'
self.assertFalse(self.gp1.generate_attribute_entry(0))
def test_str(self):
expected = "CDS (first ID=foo1)"
self.assertEquals(expected, str(self.gp2))
def test_to_gff(self):
# test .to_gff
seq_name = "sctg_0001_0001"
source = 'maker'
expected = "sctg_0001_0001\tmaker\tCDS\t1\t44\t.\t+\t.\t"
expected += "ID=foo1;Parent=mama\n"
expected += "sctg_0001_0001\tmaker\tCDS\t65\t103\t.\t+\t.\t"
expected += "ID=foo2;Parent=mama\n"
actual = self.gp2.to_gff(seq_name=seq_name, source=source)
self.assertEquals(expected, actual)
# what if no indices, etc.?
self.assertFalse(self.gp1.to_gff(seq_name="foo", source="bar"))
def test_gagflagged(self):
gp = GenePart()
self.assertFalse(gp.gagflagged())
gp.add_annotation("gag_flag", "awesome flag")
self.assertTrue(gp.gagflagged())
def test_add_annotation(self):
gp = GenePart()
self.assertFalse(gp.annotations)
gp.add_annotation("gag_flag", "this gene part rulz")
self.assertTrue(gp.annotations)