How to use test_shared method in pytest-django
Best Python code snippet using pytest-django_python
test_cgetnonuis.py
Source:test_cgetnonuis.py 
1import unittest2import test_shared 3"""4This file tests the functionality of the c_getnonuis module. 5"""6import sys7sys.path.append( '..')8sys.path.append( '.')9from nose.plugins.attrib import attr10from srmcollider import collider11from srmcollider.precursor import Precursor12from test_shared import get_non_UIS_from_transitions, getnonuis13try:14 from srmcollider import c_getnonuis15except ImportError:16 print "=" * 75, """17Module c_getnonuis is not available. Please compile it if you want to use it.18""", "=" * 7519@attr('cpp')20class Test_cgetnonuis(unittest.TestCase):21 def setUp(self):22 self.transitions = test_shared.transitions_def123 self.collisions = test_shared.collisions_def124 self.pep1 = test_shared.peptide125 self.pep2 = test_shared.peptide226 self.transitions_12_between300_1500 = test_shared.transitions_12_between300_150027 self.pep1_yseries = test_shared.pep1_yseries28 self.pep1_bseries = test_shared.pep1_bseries29 tuples = []30 tuples.append(self.pep1)31 tuples.append(self.pep2)32 self.tuples = tuple( tuples)33 class Minimal: pass34 self.par = Minimal()35 self.par.q3_window = 4.036 self.par.ppm = False37 self.q3_high = 150038 self.q3_low = 30039 self.par.bions = True40 self.par.yions = True41 self.par.aions = False42 self.par.aMinusNH3 = False43 self.par.bMinusH2O = False44 self.par.bMinusNH3 = False45 self.par.bPlusH2O = False46 self.par.yMinusH2O = False47 self.par.yMinusNH3 = False48 self.par.cions = False49 self.par.xions = False50 self.par.zions = False51 self.par.MMinusH2O = False52 self.par.MMinusNH3 = False53 def test_getnonuis(self):54 q3window = 1.055 ppm = False56 #57 result = getnonuis(self.transitions, self.collisions, q3window, ppm)58 self.assertTrue( result[201] == [1,2] )59 self.assertTrue( result[202] == [1,3] )60 self.assertTrue( result[203] == [1,2,3] )61 self.assertEqual( result, test_shared.refcollperpep1)62 #Test 263 transitions = test_shared.transitions_def264 collisions = test_shared.collisions_def265 result = getnonuis(transitions, collisions, q3window, ppm)66 self.assertTrue( result[201] == [1,2,3] )67 self.assertTrue( result[202] == [2,3,4] )68 def test_get_non_uis1(self):69 for order in range(1,6):70 res = c_getnonuis.get_non_uis(test_shared.refcollperpep1, order)71 res = set( res.keys() )72 self.assertEqual( res, test_shared.refnonuis1[order] )73 def test_get_non_uis2(self):74 for order in range(1,6):75 res = c_getnonuis.get_non_uis(test_shared.refcollperpep2, order)76 res = set( res.keys() )77 self.assertEqual( res, test_shared.refnonuis2_sorted[order] )78 def test_calculate_transitions_regular(self):79 trans = c_getnonuis.calculate_transitions_ch( (self.pep1,), [1,2], 300, 1500)80 self.assertEqual( len(trans), 10)81 for calc, ref in zip(trans, self.transitions_12_between300_1500):82 self.assertTrue(abs(calc[0] - ref) < 1e-3)83 def test_calculate_transitions_modifcation(self):84 trans = c_getnonuis.calculate_transitions_ch( (self.pep2,), [1,2], 300, 1500)85 #TODO check86 self.assertTrue(abs(trans[0][0]) - 909.333 < 1e-3)87 self.assertTrue(abs(trans[1][0]) - 780.290 < 1e-3)88 self.assertTrue(abs(trans[2][0]) - 683.238 < 1e-3)89 self.assertTrue(abs(trans[3][0]) - 523.207 < 1e-3)90 self.assertTrue(abs(trans[4][0]) - 410.123 < 1e-3)91 self.assertTrue(abs(trans[5][0]) - 330.112 < 1e-3)92 self.assertTrue(abs(trans[6][0]) - 490.143 < 1e-3)93 self.assertTrue(abs(trans[7][0]) - 603.227 < 1e-3)94 self.assertTrue(abs(trans[8][0]) - 718.254 < 1e-3)95 self.assertTrue(abs(trans[9][0]) - 865.289 < 1e-3)96 self.assertTrue(abs(trans[10][0]) - 455.170 < 1e-3) 97 self.assertTrue(abs(trans[11][0]) - 390.649 < 1e-3)98 self.assertTrue(abs(trans[12][0]) - 342.122 < 1e-3)99 self.assertTrue(abs(trans[13][0]) - 302.117 < 1e-3)100 self.assertTrue(abs(trans[14][0]) - 359.630 < 1e-3)101 self.assertTrue(abs(trans[15][0]) - 433.148 < 1e-3)102 def test_calculate_transitions_ch_regular(self):103 trans = c_getnonuis.calculate_transitions_ch( (self.pep1,), [1,2], 300, 1500)104 self.assertEqual( len(trans), 10)105 for calc, ref in zip(trans, self.transitions_12_between300_1500):106 self.assertTrue(abs(calc[0] - ref) < 1e-3)107 def test_calculate_transitions_inner(self):108 mypep = self.pep1109 transitions = c_getnonuis.calculate_transitions_ch( (mypep,), [2] , 0, 5000)110 transitions = [t[0] for t in transitions]111 self.assertEqual( len(transitions), 12)112 self.assertEqual( len(transitions), 2*len(mypep[1]) - 2 )113 y_series = transitions[:len(mypep[1])-1]114 b_series = transitions[len(mypep[1])-1:]115 self.assertEqual( len(y_series), 6)116 self.assertEqual( len(b_series), 6)117 for calc, ref in zip(y_series, self.pep1_yseries):118 self.assertTrue(abs(calc - ref) < 1e-3)119 for calc, ref in zip(b_series, self.pep1_bseries):120 self.assertTrue(abs(calc - ref) < 1e-3)121 def test_calculate_calculate_collisions_per_peptide_debug1(self):122 """123 Debug test, if there is something wrong rather not use the big ones.124 Is contained in the big test125 """126 pep = test_shared.runpep1127 transitions = test_shared.runtransitions1128 par = self.par129 q3_high = self.q3_high130 q3_low = self.q3_low131 precursors = [ 132 Precursor(q1=449.720582214, modified_sequence='SYVAWDR', transition_group=11498839L, q1_charge=2, isotopically_modified=0)133 ]134 transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])135 collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series( 136 transitions, precursors, par, q3_low, q3_high, par.q3_window, par.ppm, False)137 self.assertEqual(collisions_per_peptide,138 { 11498839: [3]} )139 def test_calculate_calculate_collisions_per_peptide_debug2(self):140 """141 Debug test, if there is something wrong rather not use the big ones.142 Is contained in the big test143 """144 pep = test_shared.runpep1145 transitions = test_shared.runtransitions1146 par = self.par147 q3_high = self.q3_high148 q3_low = self.q3_low149 precursors = [ 150 Precursor(q1=450.577779927, modified_sequence='GPGPALAGEPAGSLR', transition_group=10682370L, q1_charge=3, isotopically_modified=0),151 ]152 transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])153 collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series( 154 transitions, precursors, par, q3_low, q3_high, par.q3_window, par.ppm, False)155 self.assertEqual(collisions_per_peptide,156 {10682370: [0, 1, 2, 7, 8, 9, 11],157 })158 def test_calculate_calculate_collisions_per_peptide_debug1and2(self):159 """160 Debug test, if there is something wrong rather not use the big ones.161 Is contained in the big test162 """163 pep = test_shared.runpep1164 transitions = test_shared.runtransitions1165 par = self.par166 q3_high = self.q3_high167 q3_low = self.q3_low168 precursors = [ 169 Precursor(q1=450.577779927, modified_sequence='GPGPALAGEPAGSLR', transition_group=10682370L, q1_charge=3, isotopically_modified=0),170 Precursor(q1=449.720582214, modified_sequence='SYVAWDR', transition_group=11498839L, q1_charge=2, isotopically_modified=0)171 ]172 transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])173 collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series( 174 transitions, precursors, par, q3_low, q3_high, par.q3_window, par.ppm, False)175 self.assertEqual(collisions_per_peptide,176 {10682370: [0, 1, 2, 7, 8, 9, 11],177 11498839: [3]} )178 def test_calculate_calculate_collisions_per_peptide_1(self):179 pep = test_shared.runpep1180 transitions = test_shared.runtransitions1181 precursors = test_shared.runprecursors_obj1182 par = self.par183 q3_high = self.q3_high184 q3_low = self.q3_low185 transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])186 collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series( 187 transitions, precursors, par, q3_low, q3_high, par.q3_window, par.ppm, False)188 self.assertEqual(collisions_per_peptide, test_shared.collpepresult1)189 def test_calculate_calculate_collisions_per_peptide_2(self):190 pep = test_shared.runpep2191 transitions = test_shared.runtransitions2192 precursors = test_shared.runprecursors_obj2193 par = self.par194 q3_high = self.q3_high195 q3_low = self.q3_low196 transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])197 collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series( 198 transitions, precursors, par, q3_low, q3_high, par.q3_window, par.ppm, False)199 self.assertEqual(collisions_per_peptide, test_shared.collpepresult2)200 def test_calculate_calculate_collisions_per_peptide_other_ionseries_debug1(self):201 """202 Debug test, if there is something wrong rather not use the big ones.203 Is contained in the big test204 """205 pep = test_shared.runpep1206 transitions = test_shared.runtransitions1207 #precursors = test_shared.runprecursors1208 par = self.par209 q3_high = self.q3_high210 q3_low = self.q3_low211 precursors = [Precursor(modified_sequence='SYVAWDR',212 transition_group=11498839L, isotopically_modified=0, q1_charge=2)] 213 transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])214 collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series( 215 transitions, precursors, par, q3_low, q3_high, par.q3_window, par.ppm, False)216 #217 self.assertEqual(collisions_per_peptide,218 { 11498839: [3]} )219 def test_calculate_calculate_collisions_per_peptide_1_other(self):220 pep = test_shared.runpep1221 transitions = test_shared.runtransitions1222 precursors = test_shared.runprecursors_obj1223 par = self.par224 q3_high = self.q3_high225 q3_low = self.q3_low226 transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])227 collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series( 228 transitions, precursors, par, q3_low, q3_high, par.q3_window, par.ppm, False)229 for key in collisions_per_peptide:230 self.assertEqual(collisions_per_peptide[key], test_shared.collpepresult1[key])231 self.assertEqual(len(collisions_per_peptide), len(test_shared.collpepresult1))232 self.assertEqual(collisions_per_peptide, test_shared.collpepresult1)233 def test_calculate_calculate_collisions_per_peptide_2_other(self):234 pep = test_shared.runpep2235 transitions = test_shared.runtransitions2236 precursors = test_shared.runprecursors_obj2237 par = self.par238 q3_high = self.q3_high239 q3_low = self.q3_low240 transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])241 collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series( 242 transitions, precursors, par, q3_low, q3_high, par.q3_window, par.ppm, False)243 for key in collisions_per_peptide:244 self.assertEqual(collisions_per_peptide[key], test_shared.collpepresult2[key])245 self.assertEqual(len(collisions_per_peptide), len(test_shared.collpepresult2))246 self.assertEqual(collisions_per_peptide, test_shared.collpepresult2)247 def test_calculate_calculate_collisions_per_peptide_other_ionseries_debug_part1(self):248 """249 Debug test, if there is something wrong rather not use the big ones.250 Is contained in the big test251 """252 pep = test_shared.runpep1253 transitions = test_shared.runtransitions1254 #precursors = test_shared.runprecursors1255 par = self.par256 par.bions = True257 par.yions = True258 par.aions = True259 par.aMinusNH3 = True260 par.bMinusH2O = False261 par.bMinusNH3 = False262 par.bPlusH2O = False263 par.yMinusH2O = False264 par.yMinusNH3 = False265 par.cions = False266 par.xions = True267 par.zions = True268 q3_high = self.q3_high269 q3_low = self.q3_low270 # there is a b3 350.17164 interfering with a y3 347.22949 close to transition 3271 # there is an a4 393.21384 close to transition 8272 # there is an a4-NH3 393.21384 - 17 = 376.21384 close to transition 11273 # there is an x2 316.12575 close to transition 9 274 # there is an z3 459.19925 close to transition 2275 precursors = [Precursor(modified_sequence='SYVAWDR',276 transition_group=11498839L, isotopically_modified=0, q1_charge=2)] 277 transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])278 collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series( 279 transitions, precursors, par, q3_low, q3_high, par.q3_window, par.ppm, False)280 #281 self.assertEqual(collisions_per_peptide,282 { 11498839: [2, 3, 8, 9, 11]} )283 def test_calculate_calculate_collisions_per_peptide_other_ionseries_debug_part2(self):284 """285 Debug test, if there is something wrong rather not use the big ones.286 Is contained in the big test287 """288 pep = test_shared.runpep1289 transitions = test_shared.runtransitions1290 #precursors = test_shared.runprecursors1291 par = self.par292 par.bions = False #293 par.yions = False #294 par.aions = False #295 par.aMinusNH3 = False #296 par.bMinusH2O = False297 par.bMinusNH3 = False298 par.bPlusH2O = True299 par.yMinusH2O = True300 par.yMinusNH3 = False301 par.cions = False302 par.xions = False #303 par.zions = False #304 par.MMinusH2O = False305 par.MMinusNH3 = False306 q3_high = self.q3_high307 q3_low = self.q3_low308 precursors = [Precursor(modified_sequence='SYVAWDR',309 transition_group=11498839L, isotopically_modified=0, q1_charge=2)] 310 transitions = tuple([ (t[0], i) for i,t in enumerate(transitions)])311 collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series( 312 transitions, precursors, par, q3_low, q3_high, par.q3_window, par.ppm, False)313 #314 self.assertEqual(collisions_per_peptide,315 { 11498839: [1,2,4, 8, 9 ]} )316 def test_get_charged_mass(self):317 res = c_getnonuis.calculate_charged_mass( (0, 'VASHIPNLK', 1), 1)318 self.assertTrue( abs(res - 978.57368) < 1e-4)319 res = c_getnonuis.calculate_charged_mass( (0, 'VASHIPNLK', 1), 2)320 self.assertTrue( abs(res - 489.79078) < 1e-4)321 res = c_getnonuis.calculate_charged_mass( (0, 'VASHIPNLK', 1), 3)322 self.assertTrue( abs(res - 326.86314) < 1e-4)323 res = c_getnonuis.calculate_charged_mass( (0, 'VASHIPNLK', 1), 4)324 self.assertTrue( abs(res - 245.39932) < 1e-4)325 def test_get_charged_mass(self):326 327 pep = test_shared.runpep2328 transitions = test_shared.runtransitions2329 precursors = test_shared.runprecursors_obj2330 par = self.par331 q3_high = self.q3_high332 q3_low = self.q3_low333 precursors = [ (p.q1, p.modified_sequence, p.transition_group) for p in precursors]334 colldensity = c_getnonuis.calculate_density( 335 tuple(transitions), precursors, q3_low, q3_high, par.q3_window, par.ppm)336 self.assertEqual(colldensity, [1916, 1800, 2601, 3127, 4525, 4975, 3155, 3091, 2127, 3494, 4519, 5546, 4505, 4429, 5604])337@attr('cpp')338class Test_cgetnonuis_get_non_UIS_from_transitions(unittest.TestCase):339 """ Tests the c_getnonuis module over the collider.340 By calling collider.get_non_UIS_from_transitions, we test the function341 * c_getnonuis.get_non_uis342 in tandem.343 """344 def setUp(self):345 class Minimal: pass346 self.par = Minimal()347 self.par.q3_window = 4.0348 self.par.ppm = False349 self.MAX_UIS = 5350 def test_get_non_UIS_from_transitions1(self): 351 self.transitions = test_shared.transitions_def1352 self.collisions = test_shared.collisions_def1353 newnon_uis = get_non_UIS_from_transitions(self.transitions, 354 self.collisions, self.par, self.MAX_UIS)355 newnon_uis = [set( newn.keys() ) for newn in newnon_uis]356 self.assertEqual([len(l) for l in newnon_uis[1:]], test_shared.lennonuis1)357 self.assertEqual(newnon_uis, test_shared.refnonuis1)358 def test_get_non_UIS_from_transitions2(self): 359 self.transitions = test_shared.transitions_def2360 self.collisions = test_shared.collisions_def2361 newnon_uis = get_non_UIS_from_transitions(self.transitions, 362 self.collisions, self.par, self.MAX_UIS)363 newnon_uis = [set( newn.keys() ) for newn in newnon_uis]364 self.assertEqual([len(l) for l in newnon_uis[1:]], test_shared.lennonuis2)365 self.assertEqual(newnon_uis, test_shared.refnonuis2_sorted)366 def test_get_non_UIS_from_transitions2_unsorted(self): 367 #here we have the transitions in the wrong order368 #it should still work369 self.transitions = test_shared.transitions_def2_unsorted370 self.collisions = test_shared.collisions_def2371 newnon_uis = get_non_UIS_from_transitions(self.transitions, 372 self.collisions, self.par, self.MAX_UIS)373 newnon_uis = [set( newn.keys() ) for newn in newnon_uis]374 self.assertEqual([len(l) for l in newnon_uis[1:]], test_shared.lennonuis2)375 self.assertEqual(newnon_uis, test_shared.refnonuis2_unsorted)376 def test_get_non_UIS_from_transitions3(self): 377 self.transitions = test_shared.transitions_def3378 self.collisions = test_shared.collisions_def3379 newnon_uis = get_non_UIS_from_transitions(self.transitions, 380 self.collisions, self.par, self.MAX_UIS)381 newnon_uis = [set( newn.keys() ) for newn in newnon_uis]382 self.assertEqual([len(l) for l in newnon_uis[1:]], test_shared.lennonuis3)383 self.assertEqual(newnon_uis, test_shared.refnonuis3)384 def test_get_non_UIS_from_transitions4(self): 385 self.transitions = test_shared.transitions_def4386 self.collisions = test_shared.collisions_def4387 newnon_uis = get_non_UIS_from_transitions(self.transitions, 388 self.collisions, self.par, self.MAX_UIS)389 newnon_uis = [set( newn.keys() ) for newn in newnon_uis]390 self.assertEqual([len(l) for l in newnon_uis[1:]], test_shared.lennonuis4)391 self.assertEqual(newnon_uis, test_shared.refnonuis4)392@attr('cpp')393class Test_three_peptide_example(unittest.TestCase): 394 """395 The target is YYLLDYR with these transitions and numbers396 (842.4412197, 0), y6+397 (679.3778897, 1), y5+398 (566.2938297, 2), y4+399 (453.2097697, 3), y3+400 (440.2185450, 4), b3+401 (553.3026050, 5), b4+402 (668.3295450, 6), b5+403 (831.3928750, 7) b6+ 404 The peptides GGLIVELGDK b5+ ion interferes with the targets b3+ ion which leads to 665: [4]405 The peptides NGTDGGLQVAIDAMR b9+ ion (842.4008) interferes with the targets y6+ ion406 and also the y11++ ion (565.8035) interferes with the targets y4+ ion which leads to 618: [0, 2].407 """408 def setUp(self):409 import sys410 self.acollider = collider.SRMcollider()411 self.aparamset = collider.testcase()412 self.EPSILON = 10**-5413 par = collider.SRM_parameters()414 par.q1_window = 25 / 2.0415 par.q3_window = 1 / 2.0416 par.ppm = False417 par.q3_low = 400418 par.q3_high = 1400419 par.q3_range = [par.q3_low, par.q3_high]420 par.set_default_vars()421 par.eval()422 self.real_parameters = par423 self.precursor = test_shared.ThreePeptideExample.precursor424 self.interfering_precursors = test_shared.ThreePeptideExample.interfering_precursors425 self.oldstyle_precursors = tuple([(p.q1, p.modified_sequence, p.transition_group, p.q1_charge, p.isotopically_modified) for p in self.interfering_precursors])426 def test_find_clashes_forall_other_series_by(self):427 """ Test how to calculate the transitions of the target428 nonunique = c_getnonuis._find_clashes_forall_other_series( 429 tuple(transitions), tuple(precursors), q3_low, q3_high, 430 par.q3_window, par.ppm, par, q1 - par.q1_window)431 """432 par = self.real_parameters433 q3_low, q3_high = self.real_parameters.get_q3range_transitions()434 precursor = self.precursor435 transitions = precursor.calculate_transitions(q3_low, q3_high)436 437 nonunique = c_getnonuis._find_clashes_forall_other_series( 438 tuple(transitions), self.interfering_precursors, par, q3_low, q3_high,439 par.q3_window, par.ppm, precursor.q1 - par.q1_window, False)440 self.assertEqual( len( nonunique ), 3)441 self.assertEqual( nonunique.keys(), [0,2,4] )442 self.assertTrue( abs(nonunique[0][0][0] - 842.4008) < self.EPSILON )443 self.assertTrue( abs(nonunique[0][0][1] - 506.584613) < self.EPSILON )444 self.assertEqual( nonunique[0][0][2], 0) # empty445 self.assertEqual( nonunique[0][0][3], 618) # peptide key446 self.assertEqual( nonunique[0][0][4], 'b')447 self.assertEqual( nonunique[0][0][5], 9)448 self.assertEqual( nonunique[0][0][6], 'NGTDGGLQVAIDAMR') # sequence449 self.assertEqual( nonunique[0][0][-1], 1) # charge450 self.assertTrue( abs(nonunique[2][0][0] - 565.8035) < self.EPSILON )451 self.assertEqual( nonunique[2][0][4], 'y')452 self.assertEqual( nonunique[2][0][5], 11)453 self.assertEqual( nonunique[2][0][6], 'NGTDGGLQVAIDAMR') # sequence454 self.assertEqual( nonunique[2][0][-1], 2) # charge455 self.assertTrue( abs(nonunique[4][0][0] - 440.287275) < self.EPSILON )456 self.assertTrue( abs(nonunique[4][0][1] - 500.787837374 ) < self.EPSILON )457 self.assertEqual( nonunique[4][0][2], 0) # empty458 self.assertEqual( nonunique[4][0][3], 665) # peptide key459 self.assertEqual( nonunique[4][0][4], 'b')460 self.assertEqual( nonunique[4][0][5], 5)461 self.assertEqual( nonunique[4][0][6], 'GGLIVELGDK') # sequence462 self.assertEqual( nonunique[4][0][-1], 1) # charge463 def test_find_clashes_forall_other_series(self):464 """ Test how to calculate the transitions of the target465 nonunique = c_getnonuis._find_clashes_forall_other_series( 466 tuple(transitions), tuple(precursors), q3_low, q3_high, 467 par.q3_window, par.ppm, par, q1 - par.q1_window)468 """469 par = self.real_parameters470 par.aions = True471 par.xions = True472 par.zions = True473 par.bions = False474 par.yions = False475 #par.bMinusNH3 = True476 #par.bMinusH2O = True477 #par.bPlusH2O = True478 par.q3_window = 4.5479 q3_low, q3_high = self.real_parameters.get_q3range_transitions()480 precursor = self.precursor481 transitions = precursor.calculate_transitions(q3_low, q3_high)482 483 nonunique = c_getnonuis._find_clashes_forall_other_series( 484 tuple(transitions), self.interfering_precursors, par, q3_low, q3_high,485 par.q3_window, par.ppm, precursor.q1 - par.q1_window, False)486 self.assertEqual( len( nonunique ), 4)487 self.assertEqual( nonunique.keys(), [3,4,5,6] )488 self.assertEqual( len( nonunique[3] ), 1)489 self.assertEqual( len( nonunique[4] ), 2)490 self.assertEqual( len( nonunique[5] ), 3)491 self.assertEqual( len( nonunique[6] ), 1)492 # we have one interference with 3493 self.assertTrue( abs(nonunique[3][0][0] - 456.756009652) < self.EPSILON )494 self.assertTrue( abs(nonunique[3][0][1] - 500.787837374) < self.EPSILON )495 self.assertEqual( nonunique[3][0][2], 0) # empty496 self.assertEqual( nonunique[3][0][3], 665) # peptide key497 self.assertEqual( nonunique[3][0][4], 'x')498 self.assertEqual( nonunique[3][0][5], 8)499 self.assertEqual( nonunique[3][0][6], 'GGLIVELGDK') # sequence500 self.assertEqual( nonunique[3][0][-1], 2) # charge501 # we have two interferences with 4502 self.assertTrue( abs(nonunique[4][0][0] - 443.22541272) < self.EPSILON )503 self.assertTrue( abs(nonunique[4][0][1] - 506.58461326) < self.EPSILON )504 self.assertEqual( nonunique[4][0][2], 0) # empty505 self.assertEqual( nonunique[4][0][3], 618) # peptide key506 self.assertEqual( nonunique[4][0][4], 'a')507 self.assertEqual( nonunique[4][0][5], 10)508 self.assertEqual( nonunique[4][0][6], 'NGTDGGLQVAIDAMR') # sequence509 self.assertEqual( nonunique[4][0][-1], 2) # charge510 self.assertTrue( abs(nonunique[4][1][0] - 443.7267378235) < self.EPSILON )511 self.assertTrue( abs(nonunique[4][1][1] - 506.58461326 ) < self.EPSILON )512 self.assertEqual( nonunique[4][1][2], 0) # empty513 self.assertEqual( nonunique[4][1][3], 618) # peptide key514 self.assertEqual( nonunique[4][1][4], 'z')515 self.assertEqual( nonunique[4][1][5], 8)516 self.assertEqual( nonunique[4][1][6], 'NGTDGGLQVAIDAMR') # sequence517 self.assertEqual( nonunique[4][1][-1], 2) # charge518 # we have three interferences with 5519 self.assertTrue( abs(nonunique[5][0][0] - 557.280912722) < self.EPSILON )520 self.assertEqual( nonunique[5][0][4], 'a')521 self.assertEqual( nonunique[5][0][5], 12)522 self.assertEqual( nonunique[5][0][6], 'NGTDGGLQVAIDAMR') # sequence523 self.assertEqual( nonunique[5][0][-1], 2) # charge524 self.assertTrue( abs(nonunique[5][1][0] - 550.28240465) < self.EPSILON )525 self.assertEqual( nonunique[5][1][4], 'x')526 self.assertEqual( nonunique[5][1][5], 10)527 self.assertEqual( nonunique[5][1][6], 'NGTDGGLQVAIDAMR') # sequence528 self.assertEqual( nonunique[5][1][-1], 2) # charge529 self.assertTrue( abs(nonunique[5][2][0] - 557.2902278235) < self.EPSILON )530 self.assertEqual( nonunique[5][2][4], 'z')531 self.assertEqual( nonunique[5][2][5], 11)532 self.assertEqual( nonunique[5][2][6], 'NGTDGGLQVAIDAMR') # sequence533 self.assertEqual( nonunique[5][2][-1], 2) # charge534 # we have one interference with 6535 self.assertTrue( abs(nonunique[6][0][0] - 665.327537823 ) < self.EPSILON )536 self.assertEqual( nonunique[6][0][2], 0) # empty537 self.assertEqual( nonunique[6][0][3], 618) # peptide key538 self.assertEqual( nonunique[6][0][4], 'z')539 self.assertEqual( nonunique[6][0][5], 13)540 self.assertEqual( nonunique[6][0][6], 'NGTDGGLQVAIDAMR') # sequence541 self.assertEqual( nonunique[6][0][-1], 2) # charge542if __name__ == '__main__':...
test_loader.py
Source:test_loader.py
1import unittest2import tempfile3import os4from data import loader5class LoaderTestCase(unittest.TestCase):6 def setUp(self):7 self.data_filenames = [8 os.path.join(os.path.dirname(__file__), "../../test_shared/fixtures/loan_data_a.csv"),9 os.path.join(os.path.dirname(__file__), "../../test_shared/fixtures/loan_data_b.csv"),10 os.path.join(os.path.dirname(__file__), "../../test_shared/fixtures/loan_data_c.csv"),11 os.path.join(os.path.dirname(__file__), "../../test_shared/fixtures/loan_data_large.csv")12 ]13 def test_loans_from_csv_raw(self):14 loans = loader.loans_from_csv_raw(self.data_filenames[0])15 self.assertEqual(len(loans), 6)16 first_loan = loans[0]17 last_loan = loans[5]18 self.assertEqual(first_loan["id"], '1077501')19 self.assertEqual(first_loan["home_ownership"], "RENT")20 self.assertEqual(last_loan["id"], '1075269')21 self.assertEqual(last_loan["policy_code"], '1')22 def test_loans_from_csv(self):23 loans = loader.loans_from_csv(self.data_filenames[0])24 self.assertEqual(len(loans), 6)25 first_loan = loans[0]26 last_loan = loans[5]27 self.assertEqual(first_loan["id"], 1077501)28 self.assertEqual(first_loan["home_ownership"], "RENT")29 self.assertEqual(last_loan["id"], 1075269)30 self.assertEqual(last_loan["policy_code"], 1)31 def test_loan_iter_from_csv(self):32 count = 033 for loan in loader.loan_iter_from_csv(self.data_filenames[0]):34 count +=135 self.assertEqual(count, 6)36 def test_loan_iter_from_csv_large(self):37 count = 038 for loan in loader.loan_iter_from_csv(self.data_filenames[3]):39 count += 140 self.assertEqual(count, 42535)41if __name__ == "__main__":...
test_return_by_ref.py
Source:test_return_by_ref.py
1import return_by_ref2from return_by_ref import Matrix, RowMatrix, Vector3import numpy as np4def test_shared(mat):5 m_ref = mat.ref()6 m_ref.fill(0)7 m_copy = mat.copy()8 assert np.array_equal(m_ref,m_copy)9 m_const_ref = mat.const_ref()10 assert np.array_equal(m_const_ref,m_copy)11 assert np.array_equal(m_const_ref,m_ref)12 m_ref.fill(1)13 assert not np.array_equal(m_ref,m_copy)14 assert np.array_equal(m_const_ref,m_ref)15 try:16 m_const_ref.fill(2)17 assert False18 except:19 assert True20def test_not_shared(mat):21 m_ref = mat.ref()22 m_ref.fill(100.)23 m_copy = mat.copy()24 assert not np.array_equal(m_ref,m_copy)25 m_const_ref = mat.const_ref()26 assert np.array_equal(m_const_ref,m_copy)27 assert not np.array_equal(m_const_ref,m_ref)28 m_ref.fill(10.)29 assert not np.array_equal(m_ref,m_copy)30 assert not np.array_equal(m_const_ref,m_ref)31 try:32 m_const_ref.fill(2)33 assert True34 except:35 assert False36rows = 1037cols = 3038mat = Matrix(rows,cols)39row_mat = RowMatrix(rows,cols)40vec = Vector(rows,1)41test_shared(mat)42test_shared(row_mat)43test_shared(vec)44return_by_ref.sharedMemory(False)45test_not_shared(mat)46test_not_shared(row_mat)...
Automation Testing Tutorials
Learn to execute automation testing from scratch with LambdaTest Learning Hub. Right from setting up the prerequisites to run your first automation test, to following best practices and diving deeper into advanced test scenarios. LambdaTest Learning Hubs compile a list of step-by-step guides to help you be proficient with different test automation frameworks i.e. Selenium, Cypress, TestNG etc.
LambdaTest Learning Hubs:
- JUnit Tutorial
- TestNG Tutorial
- Webdriver Tutorial
- WebDriverIO Tutorial
- Protractor Tutorial
- Selenium 4 Tutorial
- Jenkins Tutorial
- NUnit Tutorial
- Jest Tutorial
- Playwright Tutorial
- Cypress Tutorial
- PyTest Tutorial
YouTube
You could also refer to video tutorials over LambdaTest YouTube channel to get step by step demonstration from industry experts.
Run pytest-django automation tests on LambdaTest cloud grid
Perform automation testing on 3000+ real desktop and mobile devices online.
Try LambdaTest Now !!
Get 100 minutes of automation test minutes FREE!!
Was this article helpful?
