def test_read_mast_output_430_1(self):
"""tests the read_mast_output_oldstyle function"""
with open('testdata/mast430-1.out') as inputfile:
pevalues, annotations = mast.from_430_text(
inputfile.read(), ['VNG6198H', 'VNG0117H'])
self.assertEqual('VNG6198H', pevalues[0][0])
self.assertEqual('VNG0117H', pevalues[1][0])
self.assertAlmostEqual(1.98e-14, pevalues[0][1])
self.assertAlmostEqual(3.39e-12, pevalues[1][1])
self.assertAlmostEqual(8.0e-12, pevalues[0][2])
self.assertAlmostEqual(1.4e-09, pevalues[1][2])
annot1 = list(annotations['VNG6198H'])
self.assertAlmostEqual(6.6e-01, annot1[0][0])
self.assertEqual(16, annot1[0][1])
self.assertEqual(1, annot1[0][2])
annot2 = list(annotations['VNG0117H'])
self.assertAlmostEqual(2.0e-01, annot2[0][0])
self.assertAlmostEqual(24, annot2[0][1])
self.assertAlmostEqual(-1, annot2[0][2])
self.assertAlmostEqual(4.9e-01, annot2[5][0])
self.assertAlmostEqual(223, annot2[5][1])
self.assertAlmostEqual(-2, annot2[5][2])
def test_read_mast_output_430_1(self):
"""tests the read_mast_output_oldstyle function"""
with open('testdata/mast430-1.out') as inputfile:
pevalues, annotations = mast.from_430_text(
inputfile.read(), ['VNG6198H', 'VNG0117H'])
self.assertEqual('VNG6198H', pevalues[0][0])
self.assertEqual('VNG0117H', pevalues[1][0])
self.assertAlmostEqual(1.98e-14, pevalues[0][1])
self.assertAlmostEqual(3.39e-12, pevalues[1][1])
self.assertAlmostEqual(8.0e-12, pevalues[0][2])
self.assertAlmostEqual(1.4e-09, pevalues[1][2])
annot1 = list(annotations['VNG6198H'])
self.assertAlmostEqual(6.6e-01, annot1[0][0])
self.assertEqual(16, annot1[0][1])
self.assertEqual(1, annot1[0][2])
annot2 = list(annotations['VNG0117H'])
self.assertAlmostEqual(2.0e-01, annot2[0][0])
self.assertAlmostEqual(24, annot2[0][1])
self.assertAlmostEqual(-1, annot2[0][2])
self.assertAlmostEqual(4.9e-01, annot2[5][0])
self.assertAlmostEqual(223, annot2[5][1])
self.assertAlmostEqual(-2, annot2[5][2])
def test_read_mast_output_430_2(self):
"""tests the read_mast_output function, this one has some
more silly blank line placements"""
with open('testdata/mast430-2.out') as inputfile:
pevalues, annotations = mast.from_430_text(
inputfile.read(), ['NP_279634.1', 'NP_279286.1'])
self.assertTrue('NP_279634.1' in annotations)
self.assertTrue('NP_279286.1' in annotations)
def test_read_mast_output_430_2(self):
"""tests the read_mast_output function, this one has some
more silly blank line placements"""
with open('testdata/mast430-2.out') as inputfile:
pevalues, annotations = mast.from_430_text(
inputfile.read(), ['NP_279634.1', 'NP_279286.1'])
self.assertTrue('NP_279634.1' in annotations)
self.assertTrue('NP_279286.1' in annotations)
def test_read_mast_output_430_4(self):
"""tests the read_mast_output function, this has on sequence/annotation block"""
with open('testdata/mast430-4.out') as inputfile:
pevalues, annotations = mast.from_430_text(
inputfile.read(), ['NP_280363.1', 'NP_280692.1'])
pev = [pevalue for pevalue in pevalues if pevalue[0] == 'NP_280363.1']
self.assertAlmostEqual(1.0, pev[0][1])
self.assertAlmostEqual(4.0e02, pev[0][2])
self.assertTrue('NP_280363.1' not in annotations)
def test_read_mast_output_430_3(self):
"""tests the read_mast_output function, this one has an incomplete block"""
with open('testdata/mast430-3.out') as inputfile:
pevalues, annotations = mast.from_430_text(inputfile.read(),
['NP_279608.1'])
pev = [pevalue for pevalue in pevalues if pevalue[0] == 'NP_279608.1']
self.assertAlmostEqual(3.9e-08, pev[0][1])
self.assertAlmostEqual(9.61e-11, pev[0][2])
self.assertTrue('NP_279608.1' in annotations)
def test_read_mast_output_430_4(self):
"""tests the read_mast_output function, this has on sequence/annotation block"""
with open('testdata/mast430-4.out') as inputfile:
pevalues, annotations = mast.from_430_text(
inputfile.read(), ['NP_280363.1', 'NP_280692.1'])
pev = [pevalue for pevalue in pevalues if pevalue[0] == 'NP_280363.1']
self.assertAlmostEqual(1.0, pev[0][1])
self.assertAlmostEqual(4.0e02, pev[0][2])
self.assertTrue('NP_280363.1' not in annotations)
def test_read_mast_output_430_3(self):
"""tests the read_mast_output function, this one has an incomplete block"""
with open('testdata/mast430-3.out') as inputfile:
pevalues, annotations = mast.from_430_text(
inputfile.read(), ['NP_279608.1'])
pev = [pevalue for pevalue in pevalues if pevalue[0] == 'NP_279608.1']
self.assertAlmostEqual(3.9e-08, pev[0][1])
self.assertAlmostEqual(9.61e-11, pev[0][2])
self.assertTrue('NP_279608.1' in annotations)
def read_mast_output(self, mast_output, genes):
"""old-style MAST output"""
return mast_formats.from_430_text(mast_output, genes)
def read_mast_output(self, mast_output, genes):
"""old-style MAST output"""
return mast_formats.from_430_text(mast_output, genes)