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How to use test_shared method in pytest-django
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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)...
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