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#!/usr/bin/python
# -*- coding: utf-8 -*-
import unittest
from gt import FeatureNode, FeatureNodeIteratorDepthFirst, FeatureNodeIteratorDirect, GenomeNode, GTError
class FeatureNodeTestCase(unittest.TestCase):
def setUp(self):
self.fn = FeatureNode.create_new("test", "type", 100, 500, "+")
def test_repr(self):
self.assertEqual(str(self.fn),
'FeatureNode(start=100, end=500, seqid="test")')
def test_score(self):
fn = self.fn
self.assertTrue(not fn.score_is_defined())
fn.set_score(2)
self.assertTrue(fn.score_is_defined())
self.assertEqual(2, fn.get_score())
fn.unset_score()
self.assertTrue(not fn.score_is_defined())
def test_type(self):
fn = self.fn
self.assertTrue(not fn.has_type("foo"))
self.assertTrue(fn.has_type("type"))
def test_strand(self):
fn = self.fn
self.assertEqual(fn.get_strand(), "+")
def test_seqid(self):
fn = self.fn
self.assertEqual(fn.seqid, "test")
def test_start_end(self):
fn = self.fn
self.assertEqual(fn.start, 100)
self.assertEqual(fn.end, 500)
def test_attributes(self):
fn = self.fn
fn.add_attribute("test", "testval")
fn.add_attribute("test2", "testval2")
self.assertTrue("test" in fn.attribs)
self.assertTrue("test2" in fn.attribs)
nattrs = 0
for (tag, val) in fn.each_attribute():
self.assertEqual(val, fn.get_attribute(tag))
nattrs += 1
self.assertEqual(nattrs, 2)
class TestFeatureNodeChildren(unittest.TestCase):
def setUp(self):
self.fn = FeatureNode.create_new("test", "type", 100, 500, "+")
self.fn2 = FeatureNode.create_new("test", "type2", 200, 300, "+")
self.fn.add_child(self.fn2)
def test_phase(self):
fn = self.fn
self.assertEqual(fn.get_phase(), 3)
fn.set_phase(0)
self.assertEqual(fn.get_phase(), 0)
def test_fni(self):
fn = self.fn
fni = FeatureNodeIteratorDepthFirst(fn)
num_features = 0
tfn = fni.next()
while tfn:
tfn = fni.next()
num_features += 1
self.assertEqual(num_features, 2)
fn3 = FeatureNode.create_new("test", "type3", 250, 300, "+")
fn.add_child(fn3)
fni = FeatureNodeIteratorDepthFirst(fn)
num_features = 0
tfn = fni.next()
while tfn:
num_features += 1
tfn = fni.next()
self.assertEqual(num_features, 3)
def test_iterator(self):
fn = self.fn
fn3 = FeatureNode.create_new("test", "type3", 250, 300, "+")
fn4 = FeatureNode.create_new("test", "type4", 250, 300, "+")
fn.add_child(fn3)
fn.add_child(fn4)
# try object as iterator
types = []
for i, f in enumerate(fn):
types.append(f.type)
self.assertEqual(types, ["type", "type2", "type3", "type4"], types)
self.assertTrue(i == 3, i)
# try iterator method
types = []
for i, f in enumerate(fn.traverse_dfs()):
types.append(f.type)
self.assertEqual(types, ["type", "type2", "type3", "type4"], types)
self.assertTrue(i == 3, i)
# try callable object as iterator
types = []
for i, f in enumerate(fn(method="depth_first")):
types.append(f.type)
self.assertEqual(types, ["type", "type2", "type3", "type4"], types)
self.assertTrue(i == 3, i)
# direct
types = []
for i, f in enumerate(fn(method="direct")):
types.append(f.type)
self.assertEqual(types, ["type2", "type3", "type4"], types)
self.assertTrue(i == 2, i)
types = []
for i, f in enumerate(fn.traverse_direct()):
types.append(f.type)
self.assertEqual(types, ["type2", "type3", "type4"], types)
self.assertTrue(i == 2, i)
fn.depth_first = False
types = []
for i, f in enumerate(fn):
types.append(f.type)
self.assertEqual(types, ["type2", "type3", "type4"], types)
self.assertTrue(i == 2, i)
class TestFeatureNodeProperties(unittest.TestCase):
def setUp(self):
self.fn = FeatureNode.create_new("test", "type", 100, 500, "+")
def test_strand(self):
fn = self.fn
self.assertEqual("+", fn.strand)
fn.strand = "-"
self.assertEqual("-", fn.strand)
def test_score(self):
fn = self.fn
self.assertTrue(not fn.score_is_defined())
fn.score = 2
self.assertTrue(fn.score_is_defined())
self.assertEqual(2, fn.get_score())
self.assertEqual(2, fn.score)
fn.set_score(4)
self.assertEqual(2, fn.score)
def test_range(self):
fn = self.fn
self.assertEqual((100, 500), fn.range)
def test_conversion(self):
fn = self.fn
g = GenomeNode.create_from_ptr(fn.gn, True)
self.assertEqual((100, 500), g.range)
f2 = FeatureNode.create_from_ptr(g.gn, True)
self.assertEqual((100, 500), f2.range)
class TestFeatureNodeRemoveLeaf(unittest.TestCase):
def setUp(self):
seqid = "foo"
self.gene = FeatureNode.create_new(seqid, "gene", 100, 900, "+")
exon = FeatureNode.create_new(seqid, "exon", 100, 200, "+")
self.gene.add_child(exon)
intron = FeatureNode.create_new(seqid, "intron", 201, 799, "+")
self.gene.add_child(intron)
exon = FeatureNode.create_new(seqid, "exon", 800, 900, "+")
self.gene.add_child(exon)
def test_remove_leaf(self):
fin = FeatureNodeIteratorDirect(self.gene)
while True:
fn = fin.next()
if not fn:
break
if fn.get_type() == "intron":
self.gene.remove_leaf(fn)
fin = FeatureNodeIteratorDirect(self.gene)
while True:
fn = fin.next()
if not fn:
break
if fn.get_type()== "intron":
self.fail()
def test_remove_leaf_fail(self):
self.assertRaises(AttributeError, self.gene.remove_leaf, 1)
self.assertRaises(GTError, self.gene.remove_leaf, self.gene)
if __name__ == "__main__":
unittest.main()
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