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): dna1 = core.DnaSpeciesType(id='dna1', sequence_path=self.sequence_path) gene1 = eukaryote.GeneLocus(polymer=dna1, start=1, end=15) transcript1 = eukaryote.TranscriptSpeciesType( id='t1', name='transcript1', gene=gene1, type=eukaryote.TranscriptType.mRna) self.assertEqual(transcript1.id, 't1') self.assertEqual(transcript1.name, 'transcript1') self.assertEqual(transcript1.gene, gene1) self.assertEqual(transcript1.type.name, 'mRna') self.assertEqual(transcript1.exons, []) self.assertEqual(transcript1.comments, '') self.assertEqual(transcript1.references, []) self.assertEqual(transcript1.identifiers, []) exon1 = eukaryote.GenericLocus(start=1, end=1) exon2 = eukaryote.GenericLocus(start=2, end=2) transcript1.exons = [exon1, exon2] transcript2 = eukaryote.TranscriptSpeciesType(id='t2', name='transcript2', gene=gene1, exons=[exon2]) self.assertEqual(transcript1.exons, [exon1, exon2]) self.assertEqual(transcript2.exons, [exon2])
def test_get_mol_wt(self): dna1 = core.DnaSpeciesType(id='dna6', sequence_path=self.sequence_path) gene1 = eukaryote.GeneLocus(polymer=dna1, start=1, end=6) exon1 = eukaryote.GenericLocus(start=1, end=1) transcript1 = eukaryote.TranscriptSpeciesType(gene=gene1, exons=[exon1]) exp_mol_wt = \ + Bio.SeqUtils.molecular_weight(transcript1.get_seq()) \ - (transcript1.get_len() + 1) * mendeleev.element('H').atomic_weight self.assertAlmostEqual(transcript1.get_mol_wt(), exp_mol_wt, places=1) exon2 = eukaryote.GenericLocus(start=3, end=3) transcript2 = eukaryote.TranscriptSpeciesType(gene=gene1, exons=[exon2]) exp_mol_wt = \ + Bio.SeqUtils.molecular_weight(transcript2.get_seq()) \ - (transcript2.get_len() + 1) * mendeleev.element('H').atomic_weight self.assertAlmostEqual(transcript2.get_mol_wt(), exp_mol_wt, places=1) exon3 = eukaryote.GenericLocus(start=5, end=5) transcript3 = eukaryote.TranscriptSpeciesType(gene=gene1, exons=[exon3]) exp_mol_wt = \ + Bio.SeqUtils.molecular_weight(transcript3.get_seq()) \ - (transcript3.get_len() + 1) * mendeleev.element('H').atomic_weight self.assertAlmostEqual(transcript3.get_mol_wt(), exp_mol_wt, places=1) # Test using input sequence test_trans = eukaryote.TranscriptSpeciesType() exp_mol_wt = \ + Bio.SeqUtils.molecular_weight(transcript1.get_seq()) \ - (transcript1.get_len() + 1) * mendeleev.element('H').atomic_weight self.assertAlmostEqual(test_trans.get_mol_wt(seq_input=Bio.Seq.Seq('A')), exp_mol_wt, places=1)
def test_get_charge(self): dna1 = core.DnaSpeciesType(id='dna5', sequence_path=self.sequence_path) gene1 = eukaryote.GeneLocus(polymer=dna1, start=1, end=1) exon1 = eukaryote.GenericLocus(start=1, end=1) transcript1 = eukaryote.TranscriptSpeciesType(gene=gene1, exons=[exon1]) self.assertEqual(transcript1.get_charge(), -2) gene2 = eukaryote.GeneLocus(polymer=dna1, start=2, end=4) exon2_1 = eukaryote.GenericLocus(start=2, end=2) exon2_2 = eukaryote.GenericLocus(start=4, end=4) transcript2 = eukaryote.TranscriptSpeciesType(gene=gene2, exons=[exon2_1, exon2_2]) self.assertEqual(transcript2.get_charge(), -3) # Test using input sequence test_trans = eukaryote.TranscriptSpeciesType() self.assertEqual(test_trans.get_charge(seq_input=Bio.Seq.Seq('CG')), -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_get_seq(self): dna1 = core.DnaSpeciesType(id='dna2', sequence_path=self.sequence_path) gene1 = eukaryote.GeneLocus( polymer=dna1, start=1, end=15, strand=core.PolymerStrand.positive) exon1_1 = eukaryote.GenericLocus(start=1, end=4) exon1_2 = eukaryote.GenericLocus(start=7, end=8) transcript1 = eukaryote.TranscriptSpeciesType( gene=gene1, exons=[exon1_1, exon1_2]) gene2 = eukaryote.GeneLocus( polymer=dna1, start=4, end=18, strand=core.PolymerStrand.negative) exon2_1 = eukaryote.GenericLocus(start=4, end=10) exon2_2 = eukaryote.GenericLocus(start=14, end=16) transcript2 = eukaryote.TranscriptSpeciesType( gene=gene2, exons=[exon2_1, exon2_2]) self.assertEqual(transcript1.get_seq(), 'AcUGUU') self.assertEqual(transcript2.get_seq(), 'ACGGUAACUC')
def test_get_empirical_formula(self): dna1 = core.DnaSpeciesType(id='dna3', sequence_path=self.sequence_path) gene1 = eukaryote.GeneLocus(polymer=dna1, start=1, end=4) exon1 = eukaryote.GenericLocus(start=1, end=1) transcript1 = eukaryote.TranscriptSpeciesType(gene=gene1, exons=[exon1]) self.assertEqual(transcript1.get_empirical_formula(), chem.EmpiricalFormula('C10H12N5O7P')) exon2 = eukaryote.GenericLocus(start=2, end=2) transcript2 = eukaryote.TranscriptSpeciesType(gene=gene1, exons=[exon2]) self.assertEqual(transcript2.get_empirical_formula(), chem.EmpiricalFormula('C9H12N3O8P')) exon3 = eukaryote.GenericLocus(start=3, end=3) transcript3 = eukaryote.TranscriptSpeciesType(gene=gene1, exons=[exon3]) self.assertEqual(transcript3.get_empirical_formula(), chem.EmpiricalFormula('C10H12N5O8P')) exon4 = eukaryote.GenericLocus(start=4, end=4) transcript4 = eukaryote.TranscriptSpeciesType(gene=gene1, exons=[exon4]) self.assertEqual(transcript4.get_empirical_formula(), chem.EmpiricalFormula('C9H11N2O9P')) dna2 = core.DnaSpeciesType(id='dna4', sequence_path=self.sequence_path) gene2 = eukaryote.GeneLocus(polymer=dna2, start=1, end=4) exon5_1 = eukaryote.GenericLocus(start=1, end=1) exon5_2 = eukaryote.GenericLocus(start=3, end=3) transcript5 = eukaryote.TranscriptSpeciesType(gene=gene2, exons=[exon5_1, exon5_2]) self.assertEqual(transcript5.get_empirical_formula(), chem.EmpiricalFormula('C20H23N10O13P2')) # Test using input sequence test_trans = eukaryote.TranscriptSpeciesType() self.assertEqual( test_trans.get_empirical_formula(seq_input=Bio.Seq.Seq('AA')), chem.EmpiricalFormula('C20H23N10O13P2'))
def test_constructor(self): gene = eukaryote.GeneLocus(id='gene1', name='gene1', symbol='gene_1', strand=core.PolymerStrand.negative, start=1, end=2) self.assertEqual(gene.id, 'gene1') self.assertEqual(gene.name, 'gene1') self.assertEqual(gene.symbol, 'gene_1') self.assertEqual(gene.strand, core.PolymerStrand.negative) self.assertEqual(gene.start, 1) self.assertEqual(gene.end, 2) self.assertEqual(gene.comments, '') self.assertEqual(gene.references, []) self.assertEqual(gene.identifiers, [])