def test_constructor(self):
dna1 = core.DnaSpeciesType(circular=False, double_stranded=False)
gene1 = eukaryote.GeneLocus(polymer=dna1, start=9, end=15)
gene2 = eukaryote.GeneLocus(polymer=dna1, start=17, end=18)
promoter1 = 'ENSR00000172399'
promoter2 = 'ENSR00000309980'
tf1 = eukaryote.ProteinSpeciesType(id='tf1')
tf2 = eukaryote.ProteinSpeciesType(id='tf2')
reg_module1 = eukaryote.RegulatoryModule(
gene=gene1,
promoter=promoter1,
activity=eukaryote.ActivityLevel.active,
type=eukaryote.RegulationType.proximal,
transcription_factor_regulation=[
eukaryote.TranscriptionFactorRegulation(
transcription_factor=tf1,
direction=eukaryote.RegulatoryDirection.activation),
eukaryote.TranscriptionFactorRegulation(
transcription_factor=tf2,
direction=eukaryote.RegulatoryDirection.repression)
])
reg_module2 = eukaryote.RegulatoryModule(
gene=gene1,
promoter=promoter1,
activity=eukaryote.ActivityLevel.active,
type=eukaryote.RegulationType.distal,
transcription_factor_regulation=[eukaryote.TranscriptionFactorRegulation(
transcription_factor=tf1,
direction=eukaryote.RegulatoryDirection.repression)])
reg_module3 = eukaryote.RegulatoryModule(
id='rm3',
name='reg_module3',
activity=eukaryote.ActivityLevel.inactive,
gene=gene2,
promoter=promoter2)
self.assertEqual(reg_module1.gene, gene1)
self.assertEqual(reg_module1.promoter, promoter1)
self.assertEqual(reg_module1.activity.name, 'active')
self.assertEqual(reg_module1.type.value, 1)
self.assertEqual(sorted([i.transcription_factor.id for i in reg_module1.transcription_factor_regulation]),
['tf1', 'tf2'])
self.assertEqual(sorted([i.direction.name for i in reg_module1.transcription_factor_regulation]),
['activation', 'repression'])
self.assertEqual(reg_module2.gene, gene1)
self.assertEqual(reg_module2.promoter, promoter1)
self.assertEqual(reg_module2.activity.name, 'active')
self.assertEqual(reg_module2.type.value, 2)
self.assertEqual(reg_module2.transcription_factor_regulation[0].transcription_factor, tf1)
self.assertEqual(reg_module2.transcription_factor_regulation[0].direction.name, 'repression')
self.assertEqual(reg_module3.id, 'rm3')
self.assertEqual(reg_module3.activity.name, 'inactive')
self.assertEqual(reg_module3.name, 'reg_module3')
self.assertEqual(reg_module3.promoter, promoter2)
def test_constructor(self):
tf1 = eukaryote.ProteinSpeciesType(id='tf1')
tf2 = eukaryote.ProteinSpeciesType(id='tf2')
tf_reg1 = eukaryote.TranscriptionFactorRegulation(
transcription_factor=tf1,
direction=eukaryote.RegulatoryDirection.repression)
tf_reg2 = eukaryote.TranscriptionFactorRegulation(
transcription_factor=tf2,
direction=eukaryote.RegulatoryDirection.activation)
tf_reg3 = eukaryote.TranscriptionFactorRegulation(
transcription_factor=tf2,
direction=eukaryote.RegulatoryDirection.repression)
self.assertEqual(tf_reg1.transcription_factor, tf1)
self.assertEqual(tf_reg1.direction.name, 'repression')
self.assertEqual(tf_reg2.direction.name, 'activation')
self.assertEqual(tf_reg3.transcription_factor, tf2)
def test_get_charge(self):
# Default translation table used is 1 (standard)
self.assertEqual(self.prot1.get_charge(), 1)
self.assertEqual(self.prot2.get_charge(), 2)
# Test using input sequence
test_prot = eukaryote.ProteinSpeciesType()
self.assertEqual(test_prot.get_charge(seq_input=Bio.Seq.Seq('MKVLINKNEL')), 1)
self.assertEqual(test_prot.get_charge(seq_input=Bio.Seq.Seq('MKKFLLTPL')), 2)
def test_get_mol_wt(self):
# Default translation table used is 1 (standard)
self.assertAlmostEqual(self.prot1.get_mol_wt(), 1201.49, delta=0.3)
self.assertAlmostEqual(self.prot2.get_mol_wt(), 1090.43, delta=0.3)
# Test using input sequence
test_prot = eukaryote.ProteinSpeciesType()
self.assertAlmostEqual(test_prot.get_mol_wt(seq_input=Bio.Seq.Seq('MKVLINKNEL')), 1201.49, delta=0.3)
self.assertAlmostEqual(test_prot.get_mol_wt(seq_input=Bio.Seq.Seq('MKKFLLTPL')), 1090.43, delta=0.3)
def test_ComplexSpeciesType(self):
self.tmp_dirname = tempfile.mkdtemp()
sequence_path = os.path.join(self.tmp_dirname, 'test_seq.fasta')
with open(sequence_path, 'w') as f:
f.write(
'>dna1\nTTTATGAARGTNCTCATHAAYAARAAYGARCTCTAGTTTATGAARTTYAARTTYCTCCTCACNCCNCTCTAATTT\n'
)
dna1 = core.DnaSpeciesType(id='dna1', sequence_path=sequence_path)
# Protein subunit 1
gene1 = eukaryote.GeneLocus(polymer=dna1, start=1, end=36)
exon1 = eukaryote.GenericLocus(start=4, end=36)
transcript1 = eukaryote.TranscriptSpeciesType(gene=gene1,
exons=[exon1])
cds1 = eukaryote.GenericLocus(start=4, end=36)
prot1 = eukaryote.ProteinSpeciesType(transcript=transcript1,
coding_regions=[cds1])
# Protein subunit 2
gene2 = eukaryote.GeneLocus(polymer=dna1, start=37, end=75)
exon2 = eukaryote.GenericLocus(start=40, end=72)
transcript2 = eukaryote.TranscriptSpeciesType(gene=gene2,
exons=[exon2])
cds2 = eukaryote.GenericLocus(start=40, end=72)
prot2 = eukaryote.ProteinSpeciesType(transcript=transcript2,
coding_regions=[cds2])
species_coeff1 = core.SpeciesTypeCoefficient(species_type=prot1,
coefficient=2)
species_coeff2 = core.SpeciesTypeCoefficient(species_type=prot2,
coefficient=3)
complex1 = core.ComplexSpeciesType(
subunits=[species_coeff1, species_coeff2])
self.assertEqual(complex1.get_charge(), 8)
self.assertAlmostEqual(
complex1.get_mol_wt(),
(2 * prot1.get_mol_wt() + 3 * prot2.get_mol_wt()))
self.assertEqual(complex1.get_empirical_formula(),
chem.EmpiricalFormula('C292H492N64O66S5'))
shutil.rmtree(self.tmp_dirname)
def setUp(self):
self.tmp_dirname = tempfile.mkdtemp()
sequence_path = os.path.join(self.tmp_dirname, 'test_seq.fasta')
with open(sequence_path, 'w') as f:
f.write(
'>dna1\nTTTATGAARGTNCTCATHAAYAARAAYGARCTCTAGTTTATGAARTTYAARTTYCTCCTCACNCCNCTCTAATTT\n'
)
dna1 = core.DnaSpeciesType(id='dna1', sequence_path=sequence_path)
cell1 = dna1.cell = core.Cell()
gene1 = eukaryote.GeneLocus(polymer=dna1, start=1, end=36)
exon1 = eukaryote.GenericLocus(start=4, end=36)
transcript1 = eukaryote.TranscriptSpeciesType(gene=gene1,
exons=[exon1])
cds1 = eukaryote.GenericLocus(start=4, end=36)
self.prot1 = eukaryote.ProteinSpeciesType(id='prot1',
name='protein1',
uniprot='Q12X34',
transcript=transcript1,
coding_regions=[cds1])
gene2 = eukaryote.GeneLocus(polymer=dna1,
start=30,
end=75,
strand=core.PolymerStrand.positive)
exon2_1 = eukaryote.GenericLocus(start=32, end=35)
exon2_2 = eukaryote.GenericLocus(start=38, end=45)
exon2_3 = eukaryote.GenericLocus(start=49, end=54)
exon2_4 = eukaryote.GenericLocus(start=55, end=72)
exon2_5 = eukaryote.GenericLocus(start=73, end=74)
transcript2 = eukaryote.TranscriptSpeciesType(
gene=gene2, exons=[exon2_1, exon2_2, exon2_3, exon2_4, exon2_5])
cds2_2 = eukaryote.GenericLocus(start=40, end=45)
cds2_3 = eukaryote.GenericLocus(start=49, end=54)
cds2_4 = eukaryote.GenericLocus(start=55, end=72)
self.prot2 = eukaryote.ProteinSpeciesType(
id='prot2',
name='protein2',
uniprot='P12345',
cell=cell1,
transcript=transcript2,
coding_regions=[cds2_4, cds2_2, cds2_3])
def test_serialize(self):
tf1 = eukaryote.ProteinSpeciesType(id='tf1')
tf_reg1 = eukaryote.TranscriptionFactorRegulation(
transcription_factor=tf1,
direction=eukaryote.RegulatoryDirection.repression)
tf_reg2 = eukaryote.TranscriptionFactorRegulation(
transcription_factor=tf1,
direction=eukaryote.RegulatoryDirection.activation)
self.assertEqual(tf_reg1.serialize(), 'tf1:repression')
self.assertEqual(tf_reg2.serialize(), 'tf1:activation')
def test_get_empirical_formula(self):
# Default translation table used is 1 (standard)
self.assertEqual(self.prot1.get_empirical_formula(),
chem.EmpiricalFormula('C53H96N14O15S1'))
self.assertEqual(self.prot2.get_empirical_formula(),
chem.EmpiricalFormula('C53H91N11O11S1'))
# Test using input sequence
test_prot = eukaryote.ProteinSpeciesType()
self.assertEqual(test_prot.get_empirical_formula(seq_input=Bio.Seq.Seq('MKVLINKNEL')),
chem.EmpiricalFormula('C53H96N14O15S1'))
self.assertEqual(test_prot.get_empirical_formula(seq_input=Bio.Seq.Seq('MKKFLLTPL')),
chem.EmpiricalFormula('C53H91N11O11S1'))
def test_deserialize(self):
tf1 = eukaryote.ProteinSpeciesType(id='tf1')
objects = {
eukaryote.ProteinSpeciesType: {
'tf1': tf1,
},
}
result = eukaryote.TranscriptionFactorRegulation.deserialize(
'tf1:activation', objects)
self.assertEqual(result[0].transcription_factor, tf1)
self.assertEqual(result[0].direction,
eukaryote.RegulatoryDirection.activation)
self.assertEqual(result[1], None)
result = eukaryote.TranscriptionFactorRegulation.deserialize(
'tf1:repression', objects)
self.assertEqual(result[0].transcription_factor, tf1)
self.assertEqual(result[0].direction,
eukaryote.RegulatoryDirection.repression)
self.assertEqual(result[1], None)
result = eukaryote.TranscriptionFactorRegulation.deserialize(
'tf1:unknown', objects)
self.assertEqual(result[0].transcription_factor, tf1)
self.assertEqual(result[0].direction,
eukaryote.RegulatoryDirection.unknown)
self.assertEqual(result[1], None)
result = eukaryote.TranscriptionFactorRegulation.deserialize(
'tf:activation', objects)
self.assertEqual(result[0], None)
result = eukaryote.TranscriptionFactorRegulation.deserialize(
'tf1:1', objects)
self.assertEqual(result[0], None)
result = eukaryote.TranscriptionFactorRegulation.deserialize(
'tf1:error', objects)
self.assertEqual(result[0], None)
result = eukaryote.TranscriptionFactorRegulation.deserialize(
'tf1:3.6', objects)
self.assertEqual(result[0], None)
def test_constructor(self):
# defining modified protein name
mp = eukaryote.ProteinSpeciesType(id='mp')
# testing example of modification: one protein one modified site
ptm1 = eukaryote.PtmSite(id='protptm1', name='ptm1', modified_protein=mp,
type='phosphorylation', modified_residue='s145', fractional_abundance='0.5', comments='oneprot_onesite')
self.assertEqual(ptm1.id, 'protptm1')
self.assertEqual(ptm1.name, 'ptm1')
self.assertEqual(ptm1.modified_protein, mp)
self.assertEqual(ptm1.type, 'phosphorylation')
self.assertEqual(ptm1.modified_residue, 's145')
self.assertEqual(ptm1.fractional_abundance, '0.5')
self.assertEqual(ptm1.comments, 'oneprot_onesite')
self.assertEqual(ptm1.references, [])
self.assertEqual(ptm1.identifiers, [])