def test_get_linear_hydropathy(self): testSeq = sequenceParameters.SequenceParameters('ASLPEALPSEPEASPEPASLEAPLSEPLASEASEEKEKEKEKEKEKEKEKEKEKALSPELASPELASEKEKASLEAPSELAPSELALSELAPSEAPSEAL') self.assertEqual((np.array([ 0. , 0. , 0.49333333, 0.49333333, 0.59555556, 0.47555556, 0.49333333, 0.49333333, 0.41777778, 0.25555556, 0.33111111, 0.33111111, 0.37333333, 0.33111111, 0.37333333, 0.37333333, 0.37333333, 0.49333333, 0.49333333, 0.56888889, 0.49333333, 0.59555556, 0.49333333, 0.49333333, 0.41777778, 0.53777778, 0.49333333, 0.49333333, 0.49333333, 0.56888889, 0.46666667, 0.34888889, 0.28888889, 0.28 , 0.16222222, 0.09333333, 0.09333333, 0.08444444, 0.09333333, 0.08444444, 0.09333333, 0.08444444, 0.09333333, 0.08444444, 0.09333333, 0.08444444, 0.09333333, 0.08444444, 0.09333333, 0.08444444, 0.09333333, 0.08444444, 0.21111111, 0.37333333, 0.44222222, 0.48444444, 0.49333333, 0.53777778, 0.49333333, 0.49333333, 0.49333333, 0.49333333, 0.49333333, 0.49333333, 0.49333333, 0.45111111, 0.44222222, 0.28 , 0.15333333, 0.21111111, 0.27111111, 0.44222222, 0.44222222, 0.56888889, 0.49333333, 0.49333333, 0.33111111, 0.49333333, 0.49333333, 0.49333333, 0.49333333, 0.49333333, 0.49333333, 0.49333333, 0.61333333, 0.61333333, 0.61333333, 0.61333333, 0.61333333, 0.49333333, 0.49333333, 0.49333333, 0.44888889, 0.37333333, 0.39111111, 0.33111111, 0.44888889, 0.49333333, 0. , 0. ]) - testSeq.get_linear_hydropathy()[1] < 0.0001).all(), True)
def test_save_multiple_uverskyPlot2(self): rseq2 = sequenceParameters.SequenceParameters( testTools.generate_random_sequence(minLen=20, maxLen=500)) hy1 = self.rseq.get_uversky_hydropathy() mnc1 = self.rseq.get_mean_net_charge() hy2 = rseq2.get_uversky_hydropathy() mnc2 = rseq2.get_mean_net_charge() plots.save_multiple_uverskyPlot2([self.rseq, rseq2], 'tmpfiles/mult_UV.png', ['a', 'b'], 'TEST TITLE') plots.save_multiple_uverskyPlot2([self.rseq, rseq2], 'tmpfiles/mult_UV2_NO_LEGEND.png', ['a', 'b'], title='TEST TITLE', legendOn=False) plots.save_multiple_uverskyPlot2( [self.rseq, rseq2], 'tmpfiles/mult_UV2_NO_LEGEND_xLim1.png', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=1) plots.save_multiple_uverskyPlot2( [self.rseq, rseq2], 'tmpfiles/mult_UV2_NO_LEGEND_xlim2.png', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=2) plots.save_multiple_uverskyPlot2( [self.rseq, rseq2], 'tmpfiles/mult_UV2_NO_LEGEND_xlim2_ylim2.png', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=2, yLim=2) plots.save_multiple_uverskyPlot2( [self.rseq, rseq2], 'tmpfiles/mult_UV2_NO_LEGEND_xlim2_ylim2_fs_20.png', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=2, yLim=2, fontSize=20) plots.save_multiple_uverskyPlot2( [self.rseq, rseq2], 'tmpfiles/mult_UV2_NO_LEGEND_xlim2_ylim2_fs_20.pdf', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=2, yLim=2, fontSize=20, saveFormat='pdf')
def test_save_multiple_phasePlot2(self): rseq2 = sequenceParameters.SequenceParameters( testTools.generate_random_sequence(minLen=20, maxLen=500)) plots.save_multiple_phasePlot2( [self.rseq, rseq2], 'tmpfiles/mult_PP', ['a', 'b'], 'TEST TITLE') plots.save_multiple_phasePlot2( [self.rseq, rseq2], 'tmpfiles/mult_PP_NO_LEGEND', ['a', 'b'], 'TEST TITLE', False) plots.save_multiple_phasePlot2([self.rseq, rseq2], 'tmpfiles/mult_PP_NO_LEGEND_xLim1.png', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=1) plots.save_multiple_phasePlot2([self.rseq, rseq2], 'tmpfiles/mult_PP_NO_LEGEND_xlim2.png', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=2) plots.save_multiple_phasePlot2([self.rseq, rseq2], 'tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2.png', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=2, yLim=2) plots.save_multiple_phasePlot2([self.rseq, rseq2], 'tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2_fs_20.png', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=2, yLim=2, fontSize=20) plots.save_multiple_phasePlot2([self.rseq, rseq2], 'tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2_fs_20.pdf', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=2, yLim=2, fontSize=20, saveFormat='pdf')
def test_save_multiple_phasePlot(self): rseq2 = sequenceParameters.SequenceParameters( testTools.generate_random_sequence(minLen=20, maxLen=500)) fp1 = self.rseq.get_fraction_positive() fn1 = self.rseq.get_fraction_negative() fp2 = rseq2.get_fraction_positive() fn2 = rseq2.get_fraction_negative() plots.save_multiple_phasePlot([fp1, fp2], [fn1, fn2], 'tmpfiles/mult_PP', ['a', 'b'], 'TEST TITLE') plots.save_multiple_phasePlot([fp1, fp2], [fn1, fn2], 'tmpfiles/mult_PP_NO_LEGEND.png', ['a', 'b'], title='TEST TITLE', legendOn=False) plots.save_multiple_phasePlot([fp1, fp2], [fn1, fn2], 'tmpfiles/mult_PP_NO_LEGEND_xLim1.png', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=1) plots.save_multiple_phasePlot([fp1, fp2], [fn1, fn2], 'tmpfiles/mult_PP_NO_LEGEND_xlim2.png', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=2) plots.save_multiple_phasePlot( [fp1, fp2], [fn1, fn2], 'tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2.png', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=2, yLim=2) plots.save_multiple_phasePlot( [fp1, fp2], [fn1, fn2], 'tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2_fs_20.png', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=2, yLim=2, fontSize=20) plots.save_multiple_phasePlot( [fp1, fp2], [fn1, fn2], 'tmpfiles/mult_PP_NO_LEGEND_xlim2_ylim2_fs_20.pdf', ['a', 'b'], title='TEST TITLE', legendOn=False, xLim=2, yLim=2, fontSize=20, saveFormat='pdf')
def test_get_linear_FCR(self): testSeq = sequenceParameters.SequenceParameters('ASLPEALPSEPEASPEPASLEAPLSEPLASEASEEKEKEKEKEKEKEKEKEKEKALSPELASPELASEKEKASLEAPSELAPSELALSELAPSEAPSEAL') self.assertEqual((np.array([ 0. , 0. , 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.4, 0.4, 0.4, 0.2, 0.4, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.4, 0.6, 0.6, 0.8, 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 0.8, 0.6, 0.4, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.4, 0.4, 0.6, 0.8, 0.8, 0.6, 0.4, 0.4, 0.2, 0.2, 0.2, 0.4, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.4, 0.2, 0.2, 0. , 0. ]) == testSeq.get_linear_FCR()[1]).all(), True)
def test_phaseDiagramDefinitions(self): base = "EKEKEKEKEKEKEK" sequences = [] phaseplotreg = [] for extender in ['E', 'K', 'G', 'GK', 'GE']: for i in range(0, 50): if i > 20: if i % 2 == 0: continue if i > 30: if i % 3 == 0: continue sequences.append( sequenceParameters.SequenceParameters(base + extender * i)) phaseplotreg.append( sequenceParameters.SequenceParameters( base + extender * i).get_phasePlotRegion()) plots.save_multiple_phasePlot2( sequences, 'tmpfiles/check_phasePlot_regions_match', phaseplotreg)
def setUp(self): self.testObj = sequenceParameters.SequenceParameters( "MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKNEEGAPQEGILEDMPVDPDNEAYEMPSEEGYQDYEPEA")
def test_pathological_sequences(self): # first our ability to reproduce the Das paper sequences das = [ 'EKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEKEK', 'EEEKKKEEEKKKEEEKKKEEEKKKEEEKKKEEEKKKEEEKKKEEEKKKEK', 'KEKKKEKKEEKKEEKEKEKEKEEKKKEEKEKEKEKKKEEKEKEEKKEEEE', 'KEKEEKEKKKEEEEKEKKKKEEKEKEKEKEEKKEEKKKKEEKEEKEKEKE', 'KEKEKKEEKEKKEEEKKEKEKEKKKEEKKKEEKEEKKEEKKKEEKEEEKE', 'EEEKKEKKEEKEEKKEKKEKEEEKKKEKEEKKEEEKKKEKEEEEKKKKEK', 'EEEEKKKKEEEEKKKKEEEEKKKKEEEEKKKKEEEEKKKKEEEEKKKKEK', 'KKKKEEEEKKKKEEEEKKKKEEEEKKKKEEEEKKKKEEEEKKKKEEEEKE', 'EEKKEEEKEKEKEEEEEKKEKKEKKEKKKEEKEKEKKKEKKKKEKEEEKE', 'EKKKKKKEEKKKEEEEEKKKEEEKKKEKKEEKEKEEKEKKEKKEEKEEEE', 'EKEKKKKKEEEKKEKEEEEKEEEEKKKKKEKEEEKEEKKEEKEKKKEEKK', 'EKKEEEEEEKEKKEEEEKEKEKKEKEEKEKKEKKKEKKEEEKEKKKKEKK', 'KEKKKEKEKKEKKKEEEKKKEEEKEKKKEEKKEKKEKKEEEEEEEKEEKE', 'EKKEKEEKEEEEKKKKKEEKEKKEKKKKEKKKKKEEEEEEKEEKEKEKEE', 'KKEKKEKKKEKKEKKEEEKEKEKKEKKKKEKEKKEEEEEEEEKEEKKEEE', 'EKEKEEKKKEEKKKKEKKEKEEKKEKEKEKKEEEEEEEEEKEKKEKKKKE', 'EKEKKKKKKEKEKKKKEKEKKEKKEKEEEKEEKEKEKKEEKKEEEEEEEE', 'KEEKKEEEEEEEKEEKKKKKEKKKEKKEEEKKKEEKKKEEEEEEKKKKEK', 'EEEEEKKKKKEEEEEKKKKKEEEEEKKKKKEEEEEKKKKKEEEEEKKKKK', 'EEKEEEEEEKEEEKEEKKEEEKEKKEKKEKEEKKEKKKKKKKKKKKKEEE', 'EEEEEEEEEKEKKKKKEKEEKKKKKKEKKEKKKKEKKEEEEEEKEEEKKK', 'KEEEEKEEKEEKKKKEKEEKEKKKKKKKKKKKKEKKEEEEEEEEKEKEEE', 'EEEEEKEEEEEEEEEEEKEEKEKKKKKKEKKKKKKKEKEKKKKEKKEEKK', 'EEEEKEEEEEKEEEEEEEEEEEEKKKEEKKKKKEKKKKKKKEKKKKKKKK', 'EEEEEEEEEEEKEEEEKEEKEEKEKKKKKKKKKKKKKKKKKKEEKKEEKE', 'KEEEEEEEKEEKEEEEEEEEEKEEEEKEEKKKKKKKKKKKKKKKKKKKKE', 'KKEKKKEKKEEEEEEEEEEEEEEEEEEEEKEEKKKKKKKKKKKKKKKEKK', 'EKKKKKKKKKKKKKKKKKKKKKEEEEEEEEEEEEEEEEEEKKEEEEEKEK', 'KEEEEKEEEEEEEEEEEEEEEEEEEEEKKKKKKKKKKKKKKKKKKKKKKK', 'EEEEEEEEEEEEEEEEEEEEEEEEEKKKKKKKKKKKKKKKKKKKKKKKKK'] das_kappa = [ 0.000880589547008, 0.00256304234944, 0.0138226351796, 0.024499790002, 0.0139736279003, 0.0272607247241, 0.0450342748224, 0.0450342748224, 0.0624156640006, 0.083437842179, 0.0840461196368, 0.0864189374177, 0.0951073474213, 0.131060316051, 0.135374506326, 0.145853296103, 0.16433443748, 0.167720875959, 0.194104529923, 0.27210316789, 0.273742292347, 0.321856766152, 0.354595821897, 0.445561294563, 0.528308824282, 0.610154441657, 0.672910640197, 0.766654273884, 0.876364376789, 1.0] count = 0 for i in das: a = sequenceParameters.SequenceParameters(i) self.assertEqual( round( das_kappa[count], 12), round( a.get_kappa(), 12)) count = count + 1 Pathoseqs = [ 'EEEEEEEEEEEDDEEEEGDD', 'EEEDDEEEEDESSSSGGGEE', 'EEEEEFGLDEEDEDEDEDEE', 'EEEEEDEDEDEDEDEAGSEL', 'EEEDDEDDEDSEEDSEDDED', 'EEDAECIDDDEEDEEDEEED', 'EDDEEAEEEEEEEEEEEDED', 'DGEDEDDEDDDDDDDDDDDD', 'SEEEEEEKEEEEEEEEEEEE', 'EEKEEEEEEEEEEEEEEEDE', 'EDSNEDEEEDDEEEDEEDDE', 'DEEEDDEEEDEEDDEDDESD', 'DDDDDDDSDDQGDEDDEDEE', 'EEDDEEEEEEEEEEEEELTE', 'EEDEEDEEEEESESSDSEEE', 'EGADMEEEEEEEEEEEEEEE', 'DDDDEDDDEDDDDEDLRTDS', 'EEEEEEEEEEEEETGSNSEE', 'SDSDSEEEDDEEEDDEDEDD', 'EGLGVQGAEEEEEEEEEEEE', 'ESEEGQEDEDEEDEEDEDEE', 'DEDEEEEDEEEDEEDKDADS', 'EEEKEDEEEEEEEEEEEEEE', 'DEEEEEEEEEEEEEEEVTEV', 'EPIEEEEEEEEEEEEEEEED', 'EEEEEEEEEEEEEEDQDMDA', 'ESDEEEEEEEEEEEEEDDDD', 'EEEEEEEEEEEDDDDDKGDG', 'DDEDDEESDEEEEEEEEEEE', 'EEEEEEEEEEEEATDSEEEE', 'QEEGGEEEEEEEEEEEEEEE', 'EEEEEDEEEEEEEDSIVDDA', 'EEEEDEEEEGEEGEEDEEDE', 'EQLSEEEEEEEEEEEEEEEE', 'EEEEEEEEEEEAEEEEEEED', 'DEEEDEEEEEEDEEALLEDE', 'EEEEEEEELPEDDEEEEEEE', 'EEELPEDDEEEEEEEEEDDD', 'EEEDDEDEEEEEEEEEGDGE', 'ESSEEEEEEEDEEEEEEEEE', 'EEEEEEEEEEEEEEEEEGEE', 'EENDDQEEEEEDEDDEDDEE', 'EDEEEEDDDDDDEGEDDGEE', 'PLDKACAEDDDEEDEEEEEE', 'DDEDDDEAEDNDEDEDDDEE', 'DEDDDEDGEDVEDEEEEEEE', 'EDGEDVEDEEEEEEEEEEEE', 'EEEEEEEEEEEEEEEEAAPD', 'EEEEEEEEQEEEEEEEEEEE', 'EEDEDEDLEEEEEEEEEDDD', 'EEEEGGGQGEEEEEEEEDEE', 'EEEEEEEDDEDEDADISLEE', 'DDDDDDEEDDDEDDDDDDFD', 'DEEEDDDSEEDEEDDEDEDE', 'EEEEEEEEEEEEEDFEEEEE', 'EEEEEDEEEYFEEEEEEEEE', 'EEEEGELEEEEEEEDEEEEE', 'DSSSSSEDEEEEEEEEEDED', 'ELGYPREEDEEEEEDDEEEE', 'DLGEEEEEEEEEDEEEEEDD', 'EEDEEEEEDDDDDELEDEGE', 'EDEEEEEEEEEEEKEEEEEW', 'EEAEEEEEEDEEEEEEEEEE', 'DDDDDDDEEDGVFDDEDEEE', 'EEEEEEEEEAPVSVWDEEED', 'EDDDDDDDEDDDDEEENAED', 'EDEEEEEEEEEEDEDEDLEE', 'EEEDDDEDEDEEDDVSEGSE', 'EEEEEEEEEEEEEEEAEEEE', 'DEEEEEEEEEYDEEEEEEDD', 'DEDDEDEDEDEDEDEDEDKE', 'DEDEDEDEDEDEDKEEEEED', 'DASDNEEEEEEEEEEEEEEE', 'EEVDQQEEEEEEEEEEEEEE', 'EEEEEEEEEEEAAAAVALGE', 'EDEDDEDEDEEEEDDENGDS', 'ENEEDDEDEDDDEDDDEDED', 'DEDEDDDEDDDEDEDNESEG', 'EVDEDGEEEEEEEEEEEEEE', 'EEEEEEEEEEEEEEEEYEQD', 'EEEEEEDGHSEQEEEEEEEE', 'EEDDKEDDDDDEDDDDEEDE', 'DEEDEEEEEEEEEDDDDDTE', 'EMEESEEDEEEEDEEEEEED', 'EEDEEEEEEDEEESKAGGED', 'EEEEEAEEEEEEEEEEEEEE', 'EERNGLEEEEEDDEEDEEDD'] for i in Pathoseqs: a = sequenceParameters.SequenceParameters(i) self.assertGreaterEqual(1, a.get_kappa())
def test_general_coverage(self): AAs = list("QWERTYIPASDFGHKLCVNM") # generate 5 random sequences # LENGTH BETWEEN 1 AND 150 random.seed() seq_list = [] for i in range(0, 10): L1 = random.randrange(200, 1000) S1 = "" for i in range(0, L1): S1 = S1 + random.choice(AAs) seq_list.append(S1) pos = 0 print("") # generate a list of 10 random sequences between # length 100 and 1000 seq_list = testTools.generate_random_sequence_list(number=10, minLen=100, maxLen=1000) # some edge cases... seq_list.extend(testTools.generate_random_sequence_list(number=1, minLen=3, maxLen=3)) seq_list.extend(testTools.generate_random_sequence_list(number=1, minLen=4, maxLen=4)) seq_list.extend(testTools.generate_random_sequence_list(number=1, minLen=5, maxLen=5)) seq_list.extend(testTools.generate_random_sequence_list(number=1, minLen=6, maxLen=6)) seq_list.extend(testTools.generate_random_sequence_list(number=1, minLen=7, maxLen=7)) seq_list.extend(testTools.generate_random_sequence_list(number=1, minLen=8, maxLen=8)) seq_list.extend(testTools.generate_random_sequence_list(number=1, minLen=9, maxLen=9)) seq_list.extend(testTools.generate_random_sequence_list(number=1, minLen=10, maxLen=10)) seq_list.extend(testTools.generate_random_sequence_list(number=1, minLen=11, maxLen=11)) seq_list.extend(testTools.generate_random_sequence_list(number=1, minLen=12, maxLen=12)) seq_list.append('EEEEEEEEEE') seq_list.append('KKKKKKKKKK') seq_list.append('EKEKEKEKEK') seq_list.append('GGGGGGGGGG') seq_list.append('EEEE') seq_list.append('KKKK') seq_list.append('EKEK') seq_list.append('GGGG') seq_list.append('EEEEE') seq_list.append('KKKKK') seq_list.append('EKEKE') seq_list.append('GGGGG') for i in seq_list: print("") print("Sequence " + str(pos)) print(i) iSEQ = sequenceParameters.SequenceParameters(i) iSEQ.get_FCR() iSEQ.get_FCR(pH=2.0) iSEQ.get_FCR(pH=13.0) iSEQ.get_NCPR() iSEQ.get_NCPR(pH=2.0) iSEQ.get_NCPR(pH=13.0) iSEQ.get_isoelectric_point() iSEQ.get_countNeg() iSEQ.get_countPos() iSEQ.get_fraction_positive() iSEQ.get_fraction_negative() iSEQ.get_fraction_positive() iSEQ.get_fraction_negative() iSEQ.get_fraction_disorder_promoting() iSEQ.get_fraction_expanding() iSEQ.get_fraction_expanding(pH=2.0) iSEQ.get_fraction_expanding(pH=14.0) iSEQ.get_amino_acid_fractions() iSEQ.get_kappa() iSEQ.get_Omega() iSEQ.get_Omega_sequence() iSEQ.get_kappa_X(['A','K','P','G']) iSEQ.get_kappa_X(['A','K','P','G'],['R','E','F','Y']) iSEQ.get_mean_net_charge() iSEQ.get_mean_net_charge(pH=2.0) iSEQ.get_mean_net_charge(pH=14.0) iSEQ.get_phasePlotRegion() iSEQ.get_mean_hydropathy() iSEQ.get_uversky_hydropathy() iSEQ.get_HTMLColorString() iSEQ.get_PPII_propensity() iSEQ.get_PPII_propensity(mode='hilser') iSEQ.get_PPII_propensity(mode='creamer') iSEQ.get_PPII_propensity(mode='kallenbach') #iSEQ. iSEQ.get_delta() iSEQ.get_deltaMax() # check various reduced alphabets for ABS in [2,3, 4,5,6,8,10,11,12,15,18,20]: iSEQ.get_reduced_alphabet_sequence(ABS) # actually check this... self.assertEqual(iSEQ.get_length(), len(iSEQ)) # get linear vectors... max_blobsize=len(i) iSEQ.get_linear_FCR(min(5,max_blobsize)) iSEQ.get_linear_FCR(1) iSEQ.get_linear_FCR(min(10, max_blobsize)) iSEQ.get_linear_NCPR(min(5,max_blobsize)) iSEQ.get_linear_NCPR(1) iSEQ.get_linear_NCPR(min(10, max_blobsize)) iSEQ.get_linear_hydropathy(min(5,max_blobsize)) iSEQ.get_linear_hydropathy(1) iSEQ.get_linear_hydropathy(min(10, max_blobsize)) # get complexity vectors (simple checks, more in depth in the # complexity test file...) for CT in ['WF','LC','LZW']: for ABS in [2,5,10,20]: for windowsize in [1,2,3]: iSEQ.get_linear_complexity(complexityType=CT, alphabetSize=ABS, blobLen=windowsize) psites = iSEQ.get_all_phosphorylatable_sites() print("psites") print(psites) if len(psites) > 0: # grab 3 sites randomly sites = [] for i in range(0, 2): sites.append(random.choice(psites)) iSEQ.set_phosphosites(sites) iSEQ.get_kappa_after_phosphorylation() iSEQ.get_phosphosequence() iSEQ.get_full_phosphostatus_kappa_distribution() iSEQ.clear_phosphosites() # single iSEQ.save_phaseDiagramPlot("tmpfiles/phase_test_S" + str(pos)) iSEQ.save_uverskyPlot("tmpfiles/uversky_test_S" + str(pos)) # try with a blobval iSEQ.save_linearNCPR("tmpfiles/NCPR_test_S" + str(pos), min(5, max_blobsize)) iSEQ.save_linearFCR("tmpfiles/FCR_test_S" + str(pos), min(5, max_blobsize)) iSEQ.save_linearHydropathy( "tmpfiles/Hydropathy_test_S" + str(pos), min(5, max_blobsize)) iSEQ.save_linearSigma("tmpfiles/sigma_test_S" + str(pos), min(5, max_blobsize)) # try with default iSEQ.save_linearNCPR("tmpfiles/NCPR_test_S" + str(pos), min(5, max_blobsize)) iSEQ.save_linearFCR("tmpfiles/FCR_test_S" + str(pos), min(5, max_blobsize)) iSEQ.save_linearHydropathy("tmpfiles/Hydropathy_test_S" + str(pos), min(5, max_blobsize)) iSEQ.save_linearSigma("tmpfiles/sigma_test_S" + str(pos), min(5, max_blobsize)) pos = pos + 1
def setUp(self): self.rseq = sequenceParameters.SequenceParameters( testTools.generate_random_sequence(minLen=20, maxLen=500))