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python-biopython  1.60
Public Member Functions
test_prosite2.TestPrositeRead Class Reference

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Public Member Functions

def test_read4
def read4_positive
def read4_false_etc
def test_read5
def test_read6

Detailed Description

Definition at line 13 of file test_prosite2.py.


Member Function Documentation

def test_prosite2.TestPrositeRead.read4_false_etc (   self,
  record 
)

Definition at line 338 of file test_prosite2.py.

00338 
00339     def read4_false_etc(self, record):
00340         self.assertEqual(len(record.dr_false_neg), 22)
00341         self.assertEqual(record.dr_false_neg[0], ('P30169', 'ACT7_SOLTU'))
00342         self.assertEqual(record.dr_false_neg[1], ('P24263', 'ACTD_PHYPO'))
00343         self.assertEqual(record.dr_false_neg[2], ('P12431', 'ACTM_STRPU'))
00344         self.assertEqual(record.dr_false_neg[3], ('P20360', 'ACT_EUPCR'))
00345         self.assertEqual(record.dr_false_neg[4], ('P51775', 'ACT_GIALA'))
00346         self.assertEqual(record.dr_false_neg[5], ('Q754G5', 'ARP4_ASHGO'))
00347         self.assertEqual(record.dr_false_neg[6], ('Q6FJV8', 'ARP4_CANGA'))
00348         self.assertEqual(record.dr_false_neg[7], ('Q5AW89', 'ARP4_EMENI'))
00349         self.assertEqual(record.dr_false_neg[8], ('Q6CSB9', 'ARP4_KLULA'))
00350         self.assertEqual(record.dr_false_neg[9], ('Q6C061', 'ARP4_YARLI'))
00351         self.assertEqual(record.dr_false_neg[10], ('P80428', 'ARP4_YEAST'))
00352         self.assertEqual(record.dr_false_neg[11], ('Q74ZV8', 'ARP6_ASHGO'))
00353         self.assertEqual(record.dr_false_neg[12], ('Q4W9M3', 'ARP6_ASPFU'))
00354         self.assertEqual(record.dr_false_neg[13], ('Q5AP59', 'ARP6_CANAL'))
00355         self.assertEqual(record.dr_false_neg[14], ('Q6FKE7', 'ARP6_CANGA'))
00356         self.assertEqual(record.dr_false_neg[15], ('Q5KAQ4', 'ARP6_CRYNE'))
00357         self.assertEqual(record.dr_false_neg[16], ('Q6BML9', 'ARP6_DEBHA'))
00358         self.assertEqual(record.dr_false_neg[17], ('Q5AXH1', 'ARP6_EMENI'))
00359         self.assertEqual(record.dr_false_neg[18], ('Q6CJF4', 'ARP6_KLULA'))
00360         self.assertEqual(record.dr_false_neg[19], ('Q7S6X6', 'ARP6_NEUCR'))
00361         self.assertEqual(record.dr_false_neg[20], ('O94241', 'ARP6_SCHPO'))
00362         self.assertEqual(record.dr_false_neg[21], ('Q6C982', 'ARP6_YARLI'))
00363         self.assertEqual(len(record.dr_false_pos), 0)
00364         self.assertEqual(len(record.dr_potential), 26)
00365         self.assertEqual(record.dr_potential[0], ('P30170', 'ACT10_SOLTU'))
00366         self.assertEqual(record.dr_potential[1], ('P10982', 'ACT1_ABSGL'))
00367         self.assertEqual(record.dr_potential[2], ('Q96482', 'ACT1_LYCES'))
00368         self.assertEqual(record.dr_potential[3], ('P93587', 'ACT1_SOLTU'))
00369         self.assertEqual(record.dr_potential[4], ('Q96483', 'ACT2_LYCES'))
00370         self.assertEqual(record.dr_potential[5], ('P93586', 'ACT2_SOLTU'))
00371         self.assertEqual(record.dr_potential[6], ('P93374', 'ACT2_TOBAC'))
00372         self.assertEqual(record.dr_potential[7], ('Q96484', 'ACT3_LYCES'))
00373         self.assertEqual(record.dr_potential[8], ('P93373', 'ACT3_TOBAC'))
00374         self.assertEqual(record.dr_potential[9], ('Q96481', 'ACT4_LYCES'))
00375         self.assertEqual(record.dr_potential[10], ('P93585', 'ACT4_SOLTU'))
00376         self.assertEqual(record.dr_potential[11], ('P93372', 'ACT4_TOBAC'))
00377         self.assertEqual(record.dr_potential[12], ('P81228', 'ACT5_SOLTU'))
00378         self.assertEqual(record.dr_potential[13], ('P93371', 'ACT5_TOBAC'))
00379         self.assertEqual(record.dr_potential[14], ('P15986', 'ACT6_SOYBN'))
00380         self.assertEqual(record.dr_potential[15], ('P93376', 'ACT6_TOBAC'))
00381         self.assertEqual(record.dr_potential[16], ('P15987', 'ACT7_SOYBN'))
00382         self.assertEqual(record.dr_potential[17], ('P93375', 'ACT7_TOBAC'))
00383         self.assertEqual(record.dr_potential[18], ('P81229', 'ACT8_SOLTU'))
00384         self.assertEqual(record.dr_potential[19], ('P93584', 'ACT9_SOLTU'))
00385         self.assertEqual(record.dr_potential[20], ('Q92192', 'ACT_CALFI'))
00386         self.assertEqual(record.dr_potential[21], ('P80709', 'ACT_CARMA'))
00387         self.assertEqual(record.dr_potential[22], ('Q39596', 'ACT_CHERU'))
00388         self.assertEqual(record.dr_potential[23], ('Q92193', 'ACT_CRAVI'))
00389         self.assertEqual(record.dr_potential[24], ('P81085', 'ACT_PINPS'))
00390         self.assertEqual(record.dr_potential[25], ('Q11212', 'ACT_SPOLI'))
00391         self.assertEqual(len(record.dr_unknown), 0)
00392         self.assertEqual(len(record.pdb_structs), 60)
00393         self.assertEqual(record.pdb_structs[0], '1ALM')
00394         self.assertEqual(record.pdb_structs[1], '1ATN')
00395         self.assertEqual(record.pdb_structs[2], '1C0F')
00396         self.assertEqual(record.pdb_structs[3], '1C0G')
00397         self.assertEqual(record.pdb_structs[4], '1D4X')
00398         self.assertEqual(record.pdb_structs[5], '1DEJ')
00399         self.assertEqual(record.pdb_structs[6], '1EQY')
00400         self.assertEqual(record.pdb_structs[7], '1ESV')
00401         self.assertEqual(record.pdb_structs[8], '1H1V')
00402         self.assertEqual(record.pdb_structs[9], '1HLU')
00403         self.assertEqual(record.pdb_structs[10], '1IJJ')
00404         self.assertEqual(record.pdb_structs[11], '1J6Z')
00405         self.assertEqual(record.pdb_structs[12], '1KXP')
00406         self.assertEqual(record.pdb_structs[13], '1LCU')
00407         self.assertEqual(record.pdb_structs[14], '1LOT')
00408         self.assertEqual(record.pdb_structs[15], '1LVT')
00409         self.assertEqual(record.pdb_structs[16], '1M8Q')
00410         self.assertEqual(record.pdb_structs[17], '1M8Q0')
00411         self.assertEqual(record.pdb_structs[18], '1MA9')
00412         self.assertEqual(record.pdb_structs[19], '1MDU')
00413         self.assertEqual(record.pdb_structs[20], '1MVW')
00414         self.assertEqual(record.pdb_structs[21], '1N58')
00415         self.assertEqual(record.pdb_structs[22], '1NLV')
00416         self.assertEqual(record.pdb_structs[23], '1NM1')
00417         self.assertEqual(record.pdb_structs[24], '1NMD')
00418         self.assertEqual(record.pdb_structs[25], '1NWK')
00419         self.assertEqual(record.pdb_structs[26], '1O18')
00420         self.assertEqual(record.pdb_structs[27], '1O19')
00421         self.assertEqual(record.pdb_structs[28], '1O1A')
00422         self.assertEqual(record.pdb_structs[29], '1O1B')
00423         self.assertEqual(record.pdb_structs[30], '1O1B0')
00424         self.assertEqual(record.pdb_structs[31], '1O1C')
00425         self.assertEqual(record.pdb_structs[32], '1O1C0')
00426         self.assertEqual(record.pdb_structs[33], '1O1D')
00427         self.assertEqual(record.pdb_structs[34], '1O1D0')
00428         self.assertEqual(record.pdb_structs[35], '1O1E')
00429         self.assertEqual(record.pdb_structs[36], '1O1F')
00430         self.assertEqual(record.pdb_structs[37], '1O1F0')
00431         self.assertEqual(record.pdb_structs[38], '1O1G')
00432         self.assertEqual(record.pdb_structs[39], '1P8Z')
00433         self.assertEqual(record.pdb_structs[40], '1QZ5')
00434         self.assertEqual(record.pdb_structs[41], '1QZ6')
00435         self.assertEqual(record.pdb_structs[42], '1RDW')
00436         self.assertEqual(record.pdb_structs[43], '1RFQ')
00437         self.assertEqual(record.pdb_structs[44], '1RGI')
00438         self.assertEqual(record.pdb_structs[45], '1S22')
00439         self.assertEqual(record.pdb_structs[46], '1SQK')
00440         self.assertEqual(record.pdb_structs[47], '1T44')
00441         self.assertEqual(record.pdb_structs[48], '1Y64')
00442         self.assertEqual(record.pdb_structs[49], '1YAG')
00443         self.assertEqual(record.pdb_structs[50], '1YVN')
00444         self.assertEqual(record.pdb_structs[51], '2A3Z')
00445         self.assertEqual(record.pdb_structs[52], '2A40')
00446         self.assertEqual(record.pdb_structs[53], '2A41')
00447         self.assertEqual(record.pdb_structs[54], '2A42')
00448         self.assertEqual(record.pdb_structs[55], '2A5X')
00449         self.assertEqual(record.pdb_structs[56], '2ASM')
00450         self.assertEqual(record.pdb_structs[57], '2ASO')
00451         self.assertEqual(record.pdb_structs[58], '2ASP')
00452         self.assertEqual(record.pdb_structs[59], '2BTF')

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def test_prosite2.TestPrositeRead.read4_positive (   self,
  record 
)

Definition at line 39 of file test_prosite2.py.

00039 
00040     def read4_positive(self, record):
00041         self.assertEqual(len(record.dr_positive), 295)
00042         self.assertEqual(record.dr_positive[0], ('O96019', 'ACL6A_HUMAN'))
00043         self.assertEqual(record.dr_positive[1], ('Q9Z2N8', 'ACL6A_MOUSE'))
00044         self.assertEqual(record.dr_positive[2], ('O94805', 'ACL6B_HUMAN'))
00045         self.assertEqual(record.dr_positive[3], ('Q99MR0', 'ACL6B_MOUSE'))
00046         self.assertEqual(record.dr_positive[4], ('P53496', 'ACT11_ARATH'))
00047         self.assertEqual(record.dr_positive[5], ('P30171', 'ACT11_SOLTU'))
00048         self.assertEqual(record.dr_positive[6], ('P53497', 'ACT12_ARATH'))
00049         self.assertEqual(record.dr_positive[7], ('P30172', 'ACT12_SOLTU'))
00050         self.assertEqual(record.dr_positive[8], ('P30173', 'ACT13_SOLTU'))
00051         self.assertEqual(record.dr_positive[9], ('P84185', 'ACT1D_ANOGA'))
00052         self.assertEqual(record.dr_positive[10], ('P02578', 'ACT1_ACACA'))
00053         self.assertEqual(record.dr_positive[11], ('P49128', 'ACT1_AEDAE'))
00054         self.assertEqual(record.dr_positive[12], ('P10671', 'ACT1_ARATH'))
00055         self.assertEqual(record.dr_positive[13], ('P18600', 'ACT1_ARTSX'))
00056         self.assertEqual(record.dr_positive[14], ('P83969', 'ACT1_BACDO'))
00057         self.assertEqual(record.dr_positive[15], ('P07836', 'ACT1_BOMMO'))
00058         self.assertEqual(record.dr_positive[16], ('P10983', 'ACT1_CAEEL'))
00059         self.assertEqual(record.dr_positive[17], ('P23343', 'ACT1_DAUCA'))
00060         self.assertEqual(record.dr_positive[18], ('P02577', 'ACT1_DICDI'))
00061         self.assertEqual(record.dr_positive[19], ('P68556', 'ACT1_DIPDE'))
00062         self.assertEqual(record.dr_positive[20], ('P10987', 'ACT1_DROME'))
00063         self.assertEqual(record.dr_positive[21], ('P35432', 'ACT1_ECHGR'))
00064         self.assertEqual(record.dr_positive[22], ('P68142', 'ACT1_FUGRU'))
00065         self.assertEqual(record.dr_positive[23], ('P53460', 'ACT1_HALRO'))
00066         self.assertEqual(record.dr_positive[24], ('P69002', 'ACT1_HELER'))
00067         self.assertEqual(record.dr_positive[25], ('P69003', 'ACT1_HELTB'))
00068         self.assertEqual(record.dr_positive[26], ('P92182', 'ACT1_LUMTE'))
00069         self.assertEqual(record.dr_positive[27], ('P53465', 'ACT1_LYTPI'))
00070         self.assertEqual(record.dr_positive[28], ('P02582', 'ACT1_MAIZE'))
00071         self.assertEqual(record.dr_positive[29], ('P27131', 'ACT1_NAEFO'))
00072         self.assertEqual(record.dr_positive[30], ('P30162', 'ACT1_ONCVO'))
00073         self.assertEqual(record.dr_positive[31], ('Q98972', 'ACT1_ORYLA'))
00074         self.assertEqual(record.dr_positive[32], ('P13362', 'ACT1_ORYSA'))
00075         self.assertEqual(record.dr_positive[33], ('P53503', 'ACT1_OXYFA'))
00076         self.assertEqual(record.dr_positive[34], ('P12715', 'ACT1_OXYNO'))
00077         self.assertEqual(record.dr_positive[35], ('P53468', 'ACT1_OXYTR'))
00078         self.assertEqual(record.dr_positive[36], ('P30164', 'ACT1_PEA'))
00079         self.assertEqual(record.dr_positive[37], ('P22131', 'ACT1_PHYIN'))
00080         self.assertEqual(record.dr_positive[38], ('P10988', 'ACT1_PLAFA'))
00081         self.assertEqual(record.dr_positive[39], ('P43239', 'ACT1_PNECA'))
00082         self.assertEqual(record.dr_positive[40], ('P41112', 'ACT1_PODCA'))
00083         self.assertEqual(record.dr_positive[41], ('O18499', 'ACT1_SACKO'))
00084         self.assertEqual(record.dr_positive[42], ('Q9Y702', 'ACT1_SCHCO'))
00085         self.assertEqual(record.dr_positive[43], ('P53470', 'ACT1_SCHMA'))
00086         self.assertEqual(record.dr_positive[44], ('P53504', 'ACT1_SORBI'))
00087         self.assertEqual(record.dr_positive[45], ('P02581', 'ACT1_SOYBN'))
00088         self.assertEqual(record.dr_positive[46], ('P10990', 'ACT1_STRFN'))
00089         self.assertEqual(record.dr_positive[47], ('Q9Y701', 'ACT1_SUIBO'))
00090         self.assertEqual(record.dr_positive[48], ('P10992', 'ACT1_TETTH'))
00091         self.assertEqual(record.dr_positive[49], ('Q05214', 'ACT1_TOBAC'))
00092         self.assertEqual(record.dr_positive[50], ('P12432', 'ACT1_TRYBB'))
00093         self.assertEqual(record.dr_positive[51], ('P04751', 'ACT1_XENLA'))
00094         self.assertEqual(record.dr_positive[52], ('P26197', 'ACT2_ABSGL'))
00095         self.assertEqual(record.dr_positive[53], ('Q96292', 'ACT2_ARATH'))
00096         self.assertEqual(record.dr_positive[54], ('P18601', 'ACT2_ARTSX'))
00097         self.assertEqual(record.dr_positive[55], ('P45885', 'ACT2_BACDO'))
00098         self.assertEqual(record.dr_positive[56], ('P07837', 'ACT2_BOMMO'))
00099         self.assertEqual(record.dr_positive[57], ('P10984', 'ACT2_CAEEL'))
00100         self.assertEqual(record.dr_positive[58], ('P23344', 'ACT2_DAUCA'))
00101         self.assertEqual(record.dr_positive[59], ('P07827', 'ACT2_DICDI'))
00102         self.assertEqual(record.dr_positive[60], ('P53456', 'ACT2_DIPDE'))
00103         self.assertEqual(record.dr_positive[61], ('P02572', 'ACT2_DROME'))
00104         self.assertEqual(record.dr_positive[62], ('Q03341', 'ACT2_ECHGR'))
00105         self.assertEqual(record.dr_positive[63], ('P53485', 'ACT2_FUGRU'))
00106         self.assertEqual(record.dr_positive[64], ('P27130', 'ACT2_HALRO'))
00107         self.assertEqual(record.dr_positive[65], ('P92176', 'ACT2_LUMTE'))
00108         self.assertEqual(record.dr_positive[66], ('P53466', 'ACT2_LYTPI'))
00109         self.assertEqual(record.dr_positive[67], ('Q25472', 'ACT2_MOLOC'))
00110         self.assertEqual(record.dr_positive[68], ('P27132', 'ACT2_NAEFO'))
00111         self.assertEqual(record.dr_positive[69], ('P30163', 'ACT2_ONCVO'))
00112         self.assertEqual(record.dr_positive[70], ('P17298', 'ACT2_ORYSA'))
00113         self.assertEqual(record.dr_positive[71], ('P02583', 'ACT2_OXYFA'))
00114         self.assertEqual(record.dr_positive[72], ('P55805', 'ACT2_OXYNO'))
00115         self.assertEqual(record.dr_positive[73], ('P53469', 'ACT2_OXYTR'))
00116         self.assertEqual(record.dr_positive[74], ('P30165', 'ACT2_PEA'))
00117         self.assertEqual(record.dr_positive[75], ('P22132', 'ACT2_PHYIN'))
00118         self.assertEqual(record.dr_positive[76], ('P14883', 'ACT2_PLAFA'))
00119         self.assertEqual(record.dr_positive[77], ('O18500', 'ACT2_SACKO'))
00120         self.assertEqual(record.dr_positive[78], ('Q9Y896', 'ACT2_SCHCO'))
00121         self.assertEqual(record.dr_positive[79], ('P53471', 'ACT2_SCHMA'))
00122         self.assertEqual(record.dr_positive[80], ('P69004', 'ACT2_STRFN'))
00123         self.assertEqual(record.dr_positive[81], ('Q9Y707', 'ACT2_SUIBO'))
00124         self.assertEqual(record.dr_positive[82], ('P10993', 'ACT2_TETPY'))
00125         self.assertEqual(record.dr_positive[83], ('P12433', 'ACT2_TRYBB'))
00126         self.assertEqual(record.dr_positive[84], ('P10995', 'ACT2_XENLA'))
00127         self.assertEqual(record.dr_positive[85], ('P20399', 'ACT2_XENTR'))
00128         self.assertEqual(record.dr_positive[86], ('Q25010', 'ACT3A_HELAM'))
00129         self.assertEqual(record.dr_positive[87], ('P84184', 'ACT3B_HELAM'))
00130         self.assertEqual(record.dr_positive[88], ('P18602', 'ACT3_ARTSX'))
00131         self.assertEqual(record.dr_positive[89], ('P45886', 'ACT3_BACDO'))
00132         self.assertEqual(record.dr_positive[90], ('P04829', 'ACT3_BOMMO'))
00133         self.assertEqual(record.dr_positive[91], ('P07829', 'ACT3_DICDI'))
00134         self.assertEqual(record.dr_positive[92], ('P53457', 'ACT3_DIPDE'))
00135         self.assertEqual(record.dr_positive[93], ('P53501', 'ACT3_DROME'))
00136         self.assertEqual(record.dr_positive[94], ('Q03342', 'ACT3_ECHGR'))
00137         self.assertEqual(record.dr_positive[95], ('P53486', 'ACT3_FUGRU'))
00138         self.assertEqual(record.dr_positive[96], ('P41340', 'ACT3_LIMPO'))
00139         self.assertEqual(record.dr_positive[97], ('Q25379', 'ACT3_LYTPI'))
00140         self.assertEqual(record.dr_positive[98], ('P17299', 'ACT3_ORYSA'))
00141         self.assertEqual(record.dr_positive[99], ('P46258', 'ACT3_PEA'))
00142         self.assertEqual(record.dr_positive[100], ('P41113', 'ACT3_PODCA'))
00143         self.assertEqual(record.dr_positive[101], ('P30167', 'ACT3_SOLTU'))
00144         self.assertEqual(record.dr_positive[102], ('P02580', 'ACT3_SOYBN'))
00145         self.assertEqual(record.dr_positive[103], ('P04752', 'ACT3_XENLA'))
00146         self.assertEqual(record.dr_positive[104], ('P53494', 'ACT4_ARATH'))
00147         self.assertEqual(record.dr_positive[105], ('P18603', 'ACT4_ARTSX'))
00148         self.assertEqual(record.dr_positive[106], ('P84183', 'ACT4_BOMMO'))
00149         self.assertEqual(record.dr_positive[107], ('P10986', 'ACT4_CAEEL'))
00150         self.assertEqual(record.dr_positive[108], ('P07828', 'ACT4_DICDI'))
00151         self.assertEqual(record.dr_positive[109], ('P02574', 'ACT4_DROME'))
00152         self.assertEqual(record.dr_positive[110], ('Q25380', 'ACT4_LYTPI'))
00153         self.assertEqual(record.dr_positive[111], ('Q8RYC2', 'ACT5_ARATH'))
00154         self.assertEqual(record.dr_positive[112], ('P45887', 'ACT5_BACDO'))
00155         self.assertEqual(record.dr_positive[113], ('P53478', 'ACT5_CHICK'))
00156         self.assertEqual(record.dr_positive[114], ('P53458', 'ACT5_DIPDE'))
00157         self.assertEqual(record.dr_positive[115], ('P10981', 'ACT5_DROME'))
00158         self.assertEqual(record.dr_positive[116], ('P53505', 'ACT5_XENLA'))
00159         self.assertEqual(record.dr_positive[117], ('P53459', 'ACT6_DIPDE'))
00160         self.assertEqual(record.dr_positive[118], ('P83967', 'ACT6_DROME'))
00161         self.assertEqual(record.dr_positive[119], ('P83968', 'ACT6_DROSI'))
00162         self.assertEqual(record.dr_positive[120], ('P30168', 'ACT6_SOLTU'))
00163         self.assertEqual(record.dr_positive[121], ('P53492', 'ACT7_ARATH'))
00164         self.assertEqual(record.dr_positive[122], ('P17300', 'ACT7_ORYSA'))
00165         self.assertEqual(record.dr_positive[123], ('Q96293', 'ACT8_ARATH'))
00166         self.assertEqual(record.dr_positive[124], ('P07830', 'ACT8_DICDI'))
00167         self.assertEqual(record.dr_positive[125], ('P53506', 'ACT8_XENLA'))
00168         self.assertEqual(record.dr_positive[126], ('P93738', 'ACT9_ARATH'))
00169         self.assertEqual(record.dr_positive[127], ('P62739', 'ACTA_BOVIN'))
00170         self.assertEqual(record.dr_positive[128], ('P08023', 'ACTA_CHICK'))
00171         self.assertEqual(record.dr_positive[129], ('P62736', 'ACTA_HUMAN'))
00172         self.assertEqual(record.dr_positive[130], ('P41339', 'ACTA_LIMPO'))
00173         self.assertEqual(record.dr_positive[131], ('P62737', 'ACTA_MOUSE'))
00174         self.assertEqual(record.dr_positive[132], ('P02576', 'ACTA_PHYPO'))
00175         self.assertEqual(record.dr_positive[133], ('P62740', 'ACTA_RABIT'))
00176         self.assertEqual(record.dr_positive[134], ('P62738', 'ACTA_RAT'))
00177         self.assertEqual(record.dr_positive[135], ('P53472', 'ACTA_STRPU'))
00178         self.assertEqual(record.dr_positive[136], ('Q7ZVI7', 'ACTB1_BRARE'))
00179         self.assertEqual(record.dr_positive[137], ('Q7ZVF9', 'ACTB2_BRARE'))
00180         self.assertEqual(record.dr_positive[138], ('P60712', 'ACTB_BOVIN'))
00181         self.assertEqual(record.dr_positive[139], ('P84336', 'ACTB_CAMDR'))
00182         self.assertEqual(record.dr_positive[140], ('O18840', 'ACTB_CANFA'))
00183         self.assertEqual(record.dr_positive[141], ('Q71FK5', 'ACTB_CAVPO'))
00184         self.assertEqual(record.dr_positive[142], ('Q76N69', 'ACTB_CERAE'))
00185         self.assertEqual(record.dr_positive[143], ('P60706', 'ACTB_CHICK'))
00186         self.assertEqual(record.dr_positive[144], ('P48975', 'ACTB_CRIGR'))
00187         self.assertEqual(record.dr_positive[145], ('P83751', 'ACTB_CTEID'))
00188         self.assertEqual(record.dr_positive[146], ('P83750', 'ACTB_CYPCA'))
00189         self.assertEqual(record.dr_positive[147], ('P60708', 'ACTB_HORSE'))
00190         self.assertEqual(record.dr_positive[148], ('P60709', 'ACTB_HUMAN'))
00191         self.assertEqual(record.dr_positive[149], ('Q711N9', 'ACTB_MESAU'))
00192         self.assertEqual(len(record.dr_positive), 295)
00193         self.assertEqual(record.dr_positive[150], ('P60710', 'ACTB_MOUSE'))
00194         self.assertEqual(record.dr_positive[151], ('P68143', 'ACTB_OREMO'))
00195         self.assertEqual(record.dr_positive[152], ('P79818', 'ACTB_ORYLA'))
00196         self.assertEqual(record.dr_positive[153], ('Q5R1X3', 'ACTB_PANTR'))
00197         self.assertEqual(record.dr_positive[154], ('P29751', 'ACTB_RABIT'))
00198         self.assertEqual(record.dr_positive[155], ('P60711', 'ACTB_RAT'))
00199         self.assertEqual(record.dr_positive[156], ('O42161', 'ACTB_SALSA'))
00200         self.assertEqual(record.dr_positive[157], ('P60713', 'ACTB_SHEEP'))
00201         self.assertEqual(record.dr_positive[158], ('Q91ZK5', 'ACTB_SIGHI'))
00202         self.assertEqual(record.dr_positive[159], ('P53473', 'ACTB_STRPU'))
00203         self.assertEqual(record.dr_positive[160], ('P60707', 'ACTB_TRIVU'))
00204         self.assertEqual(record.dr_positive[161], ('P15475', 'ACTB_XENBO'))
00205         self.assertEqual(record.dr_positive[162], ('O93400', 'ACTB_XENLA'))
00206         self.assertEqual(record.dr_positive[163], ('Q964E3', 'ACTC_BIOAL'))
00207         self.assertEqual(record.dr_positive[164], ('P92179', 'ACTC_BIOGL'))
00208         self.assertEqual(record.dr_positive[165], ('Q964E1', 'ACTC_BIOOB'))
00209         self.assertEqual(record.dr_positive[166], ('Q964E2', 'ACTC_BIOPF'))
00210         self.assertEqual(record.dr_positive[167], ('Q964E0', 'ACTC_BIOTE'))
00211         self.assertEqual(record.dr_positive[168], ('Q93129', 'ACTC_BRABE'))
00212         self.assertEqual(record.dr_positive[169], ('Q93131', 'ACTC_BRAFL'))
00213         self.assertEqual(record.dr_positive[170], ('O17503', 'ACTC_BRALA'))
00214         self.assertEqual(record.dr_positive[171], ('P68034', 'ACTC_CHICK'))
00215         self.assertEqual(record.dr_positive[172], ('P53480', 'ACTC_FUGRU'))
00216         self.assertEqual(record.dr_positive[173], ('P53461', 'ACTC_HALRO'))
00217         self.assertEqual(record.dr_positive[174], ('Q964D9', 'ACTC_HELTI'))
00218         self.assertEqual(record.dr_positive[175], ('P68032', 'ACTC_HUMAN'))
00219         self.assertEqual(record.dr_positive[176], ('P68033', 'ACTC_MOUSE'))
00220         self.assertEqual(record.dr_positive[177], ('P12716', 'ACTC_PISOC'))
00221         self.assertEqual(record.dr_positive[178], ('P68035', 'ACTC_RAT'))
00222         self.assertEqual(record.dr_positive[179], ('Q07903', 'ACTC_STRPU'))
00223         self.assertEqual(record.dr_positive[180], ('Q00215', 'ACTC_STYPL'))
00224         self.assertEqual(record.dr_positive[181], ('P69005', 'ACTD_STRPU'))
00225         self.assertEqual(record.dr_positive[182], ('P53474', 'ACTE_STRPU'))
00226         self.assertEqual(record.dr_positive[183], ('P18499', 'ACTF_STRPU'))
00227         self.assertEqual(record.dr_positive[184], ('P63256', 'ACTG_ANSAN'))
00228         self.assertEqual(record.dr_positive[185], ('P63258', 'ACTG_BOVIN'))
00229         self.assertEqual(record.dr_positive[186], ('Q9UVW9', 'ACTG_CEPAC'))
00230         self.assertEqual(record.dr_positive[187], ('P20359', 'ACTG_EMENI'))
00231         self.assertEqual(record.dr_positive[188], ('P63261', 'ACTG_HUMAN'))
00232         self.assertEqual(record.dr_positive[189], ('P63260', 'ACTG_MOUSE'))
00233         self.assertEqual(record.dr_positive[190], ('Q9URS0', 'ACTG_PENCH'))
00234         self.assertEqual(record.dr_positive[191], ('P63259', 'ACTG_RAT'))
00235         self.assertEqual(record.dr_positive[192], ('P63257', 'ACTG_TRIVU'))
00236         self.assertEqual(record.dr_positive[193], ('P63270', 'ACTH_CHICK'))
00237         self.assertEqual(record.dr_positive[194], ('P63267', 'ACTH_HUMAN'))
00238         self.assertEqual(record.dr_positive[195], ('P63268', 'ACTH_MOUSE'))
00239         self.assertEqual(record.dr_positive[196], ('P63269', 'ACTH_RAT'))
00240         self.assertEqual(record.dr_positive[197], ('P17304', 'ACTM_APLCA'))
00241         self.assertEqual(record.dr_positive[198], ('Q93130', 'ACTM_BRABE'))
00242         self.assertEqual(record.dr_positive[199], ('Q93132', 'ACTM_BRAFL'))
00243         self.assertEqual(record.dr_positive[200], ('O17502', 'ACTM_BRALA'))
00244         self.assertEqual(record.dr_positive[201], ('O15998', 'ACTM_CIOSA'))
00245         self.assertEqual(record.dr_positive[202], ('P53463', 'ACTM_HELER'))
00246         self.assertEqual(record.dr_positive[203], ('P53464', 'ACTM_HELTB'))
00247         self.assertEqual(record.dr_positive[204], ('Q25381', 'ACTM_LYTPI'))
00248         self.assertEqual(record.dr_positive[205], ('P53467', 'ACTM_MOLOC'))
00249         self.assertEqual(record.dr_positive[206], ('P12717', 'ACTM_PISOC'))
00250         self.assertEqual(record.dr_positive[207], ('P26198', 'ACTM_STYCL'))
00251         self.assertEqual(record.dr_positive[208], ('Q00214', 'ACTM_STYPL'))
00252         self.assertEqual(record.dr_positive[209], ('P53475', 'ACTN_STYCL'))
00253         self.assertEqual(record.dr_positive[210], ('Q90X97', 'ACTS_ATRMM'))
00254         self.assertEqual(record.dr_positive[211], ('P68138', 'ACTS_BOVIN'))
00255         self.assertEqual(record.dr_positive[212], ('P49055', 'ACTS_CARAU'))
00256         self.assertEqual(record.dr_positive[213], ('P68139', 'ACTS_CHICK'))
00257         self.assertEqual(record.dr_positive[214], ('P53479', 'ACTS_CYPCA'))
00258         self.assertEqual(record.dr_positive[215], ('P68140', 'ACTS_FUGRU'))
00259         self.assertEqual(record.dr_positive[216], ('P68133', 'ACTS_HUMAN'))
00260         self.assertEqual(record.dr_positive[217], ('P68134', 'ACTS_MOUSE'))
00261         self.assertEqual(record.dr_positive[218], ('P68264', 'ACTS_OREMO'))
00262         self.assertEqual(record.dr_positive[219], ('P68137', 'ACTS_PIG'))
00263         self.assertEqual(record.dr_positive[220], ('P10994', 'ACTS_PLEWA'))
00264         self.assertEqual(record.dr_positive[221], ('P68135', 'ACTS_RABIT'))
00265         self.assertEqual(record.dr_positive[222], ('P68136', 'ACTS_RAT'))
00266         self.assertEqual(record.dr_positive[223], ('P53482', 'ACTT_FUGRU'))
00267         self.assertEqual(record.dr_positive[224], ('P53483', 'ACTX_FUGRU'))
00268         self.assertEqual(record.dr_positive[225], ('P42025', 'ACTY_HUMAN'))
00269         self.assertEqual(record.dr_positive[226], ('P41341', 'ACTY_LIMPO'))
00270         self.assertEqual(record.dr_positive[227], ('Q8R5C5', 'ACTY_MOUSE'))
00271         self.assertEqual(record.dr_positive[228], ('P61162', 'ACTZ_CANFA'))
00272         self.assertEqual(record.dr_positive[229], ('P45889', 'ACTZ_DROME'))
00273         self.assertEqual(record.dr_positive[230], ('P61163', 'ACTZ_HUMAN'))
00274         self.assertEqual(record.dr_positive[231], ('P61164', 'ACTZ_MOUSE'))
00275         self.assertEqual(record.dr_positive[232], ('P53491', 'ACT_ACECL'))
00276         self.assertEqual(record.dr_positive[233], ('P26182', 'ACT_ACHBI'))
00277         self.assertEqual(record.dr_positive[234], ('P53455', 'ACT_AJECA'))
00278         self.assertEqual(record.dr_positive[235], ('Q75D00', 'ACT_ASHGO'))
00279         self.assertEqual(record.dr_positive[236], ('O13419', 'ACT_BOTCI'))
00280         self.assertEqual(record.dr_positive[237], ('P90689', 'ACT_BRUMA'))
00281         self.assertEqual(record.dr_positive[238], ('P14235', 'ACT_CANAL'))
00282         self.assertEqual(record.dr_positive[239], ('Q9UVZ8', 'ACT_CANDU'))
00283         self.assertEqual(record.dr_positive[240], ('P60009', 'ACT_CANGA'))
00284         self.assertEqual(record.dr_positive[241], ('P53498', 'ACT_CHLRE'))
00285         self.assertEqual(record.dr_positive[242], ('P53499', 'ACT_CHOCR'))
00286         self.assertEqual(record.dr_positive[243], ('O65315', 'ACT_COLSC'))
00287         self.assertEqual(record.dr_positive[244], ('Q9UVX4', 'ACT_COPCI'))
00288         self.assertEqual(record.dr_positive[245], ('P30161', 'ACT_COSCS'))
00289         self.assertEqual(record.dr_positive[246], ('O17320', 'ACT_CRAGI'))
00290         self.assertEqual(record.dr_positive[247], ('P48465', 'ACT_CRYNV'))
00291         self.assertEqual(record.dr_positive[248], ('P26183', 'ACT_CRYPV'))
00292         self.assertEqual(record.dr_positive[249], ('P53500', 'ACT_CYAME'))
00293         self.assertEqual(record.dr_positive[250], ('Q24733', 'ACT_DICVI'))
00294         self.assertEqual(record.dr_positive[251], ('P11426', 'ACT_ENTHI'))
00295         self.assertEqual(record.dr_positive[252], ('Q8X119', 'ACT_EXODE'))
00296         self.assertEqual(record.dr_positive[253], ('P53502', 'ACT_FUCDI'))
00297         self.assertEqual(record.dr_positive[254], ('Q39758', 'ACT_FUCVE'))
00298         self.assertEqual(record.dr_positive[255], ('Q6TCF2', 'ACT_GAEGA'))
00299         self.assertEqual(record.dr_positive[256], ('O81221', 'ACT_GOSHI'))
00300         self.assertEqual(record.dr_positive[257], ('O00937', 'ACT_HISCA'))
00301         self.assertEqual(record.dr_positive[258], ('P17126', 'ACT_HYDAT'))
00302         self.assertEqual(record.dr_positive[259], ('P17128', 'ACT_KLULA'))
00303         self.assertEqual(record.dr_positive[260], ('P45520', 'ACT_LEIMA'))
00304         self.assertEqual(record.dr_positive[261], ('P91754', 'ACT_LUMRU'))
00305         self.assertEqual(record.dr_positive[262], ('P49871', 'ACT_MANSE'))
00306         self.assertEqual(record.dr_positive[263], ('O16808', 'ACT_MAYDE'))
00307         self.assertEqual(record.dr_positive[264], ('O65316', 'ACT_MESVI'))
00308         self.assertEqual(record.dr_positive[265], ('P78711', 'ACT_NEUCR'))
00309         self.assertEqual(record.dr_positive[266], ('P53689', 'ACT_PHARH'))
00310         self.assertEqual(record.dr_positive[267], ('P13363', 'ACT_PHYME'))
00311         self.assertEqual(record.dr_positive[268], ('O74258', 'ACT_PICAN'))
00312         self.assertEqual(record.dr_positive[269], ('Q9P4D1', 'ACT_PICPA'))
00313         self.assertEqual(record.dr_positive[270], ('P24902', 'ACT_PINCO'))
00314         self.assertEqual(record.dr_positive[271], ('Q26065', 'ACT_PLAMG'))
00315         self.assertEqual(record.dr_positive[272], ('P45521', 'ACT_PROCL'))
00316         self.assertEqual(record.dr_positive[273], ('P50138', 'ACT_PUCGR'))
00317         self.assertEqual(record.dr_positive[274], ('P60011', 'ACT_SACBA'))
00318         self.assertEqual(record.dr_positive[275], ('O65314', 'ACT_SCHDU'))
00319         self.assertEqual(record.dr_positive[276], ('P10989', 'ACT_SCHPO'))
00320         self.assertEqual(record.dr_positive[277], ('P68555', 'ACT_TAESO'))
00321         self.assertEqual(record.dr_positive[278], ('P10365', 'ACT_THELA'))
00322         self.assertEqual(record.dr_positive[279], ('P53476', 'ACT_TOXGO'))
00323         self.assertEqual(record.dr_positive[280], ('Q99023', 'ACT_TRIRE'))
00324         self.assertEqual(record.dr_positive[281], ('P53477', 'ACT_TRYCR'))
00325         self.assertEqual(record.dr_positive[282], ('P20904', 'ACT_VOLCA'))
00326         self.assertEqual(record.dr_positive[283], ('Q9UVF3', 'ACT_YARLI'))
00327         self.assertEqual(record.dr_positive[284], ('P60010', 'ACT_YEAST'))
00328         self.assertEqual(record.dr_positive[285], ('Q61JZ2', 'ARP2_CAEBR'))
00329         self.assertEqual(record.dr_positive[286], ('P53489', 'ARP2_CAEEL'))
00330         self.assertEqual(record.dr_positive[287], ('Q4WHA3', 'ARP4_ASPFU'))
00331         self.assertEqual(record.dr_positive[288], ('Q5AC48', 'ARP4_CANAL'))
00332         self.assertEqual(record.dr_positive[289], ('Q6BXN0', 'ARP4_DEBHA'))
00333         self.assertEqual(record.dr_positive[290], ('Q4IPI4', 'ARP4_GIBZE'))
00334         self.assertEqual(record.dr_positive[291], ('Q7SHR0', 'ARP4_NEUCR'))
00335         self.assertEqual(record.dr_positive[292], ('Q9P7X7', 'ARP4_SCHPO'))
00336         self.assertEqual(record.dr_positive[293], ('Q4P2E8', 'ARP4_USTMA'))
00337         self.assertEqual(record.dr_positive[294], ('Q09849', 'YAE9_SCHPO'))

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Definition at line 15 of file test_prosite2.py.

00015 
00016     def test_read4(self):
00017         "Parsing Prosite record ps00432.txt"
00018         filename = os.path.join('Prosite', 'ps00432.txt')
00019         handle = open(filename)
00020         record = Prosite.read(handle)
00021         self.assertEqual(record.name, "ACTINS_2")
00022         self.assertEqual(record.type, "PATTERN")
00023         self.assertEqual(record.accession, "PS00432")
00024         self.assertEqual(record.created, "NOV-1990")
00025         self.assertEqual(record.data_update, "DEC-2004")
00026         self.assertEqual(record.info_update, "MAR-2006")
00027         self.assertEqual(record.pdoc, "PDOC00340")
00028         self.assertEqual(record.description, "Actins signature 2.")
00029         self.assertEqual(record.pattern, "W-[IVC]-[STAK]-[RK]-x-[DE]-Y-[DNE]-[DE].")
00030         self.assertEqual(record.matrix, [])
00031         self.assertEqual(record.rules, [])
00032         self.assertEqual(record.nr_sp_release, "49.3")
00033         self.assertEqual(record.nr_sp_seqs, 212425)
00034         self.assertEqual(record.cc_taxo_range, "??E??")
00035         self.assertEqual(record.cc_max_repeat, "1")
00036         self.assertEqual(len(record.cc_site), 0)
00037         self.read4_positive(record)
00038         self.read4_false_etc(record)

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Definition at line 453 of file test_prosite2.py.

00453 
00454     def test_read5(self):
00455         "Parsing Prosite record ps00488.txt"
00456         filename = os.path.join('Prosite', 'ps00488.txt')
00457         handle = open(filename)
00458         record = Prosite.read(handle)
00459         self.assertEqual(record.name, "PAL_HISTIDASE")
00460         self.assertEqual(record.type, "PATTERN")
00461         self.assertEqual(record.accession, "PS00488")
00462         self.assertEqual(record.created, "MAY-1991")
00463         self.assertEqual(record.data_update, "DEC-2004")
00464         self.assertEqual(record.info_update, "MAR-2006")
00465         self.assertEqual(record.pdoc, "PDOC00424")
00466         self.assertEqual(record.description, "Phenylalanine and histidine ammonia-lyases signature.")
00467         self.assertEqual(record.pattern, "[GS]-[STG]-[LIVM]-[STG]-[SAC]-S-G-[DH]-L-x-P-L-[SA]-x(2,3)-[SAGVT].")
00468         self.assertEqual(record.matrix, [])
00469         self.assertEqual(record.rules, [])
00470         self.assertEqual(record.nr_sp_release, "49.3")
00471         self.assertEqual(record.nr_sp_seqs, 212425)
00472         self.assertEqual(record.cc_taxo_range, "A?EP?")
00473         self.assertEqual(record.cc_max_repeat, "1")
00474         self.assertEqual(len(record.cc_site), 1)
00475         self.assertEqual(record.cc_site[0], (6, 'active_site'))
00476         self.assertEqual(len(record.dr_positive), 127)
00477         self.assertEqual(record.dr_positive[0], ('Q8RFC2', 'HUTH1_FUSNN'))
00478         self.assertEqual(record.dr_positive[1], ('Q8RDU4', 'HUTH2_FUSNN'))
00479         self.assertEqual(record.dr_positive[2], ('Q9KWE4', 'HUTH_AGRRH'))
00480         self.assertEqual(record.dr_positive[3], ('Q8U8Z7', 'HUTH_AGRT5'))
00481         self.assertEqual(record.dr_positive[4], ('Q5NZX8', 'HUTH_AZOSE'))
00482         self.assertEqual(record.dr_positive[5], ('Q81Y45', 'HUTH_BACAN'))
00483         self.assertEqual(record.dr_positive[6], ('Q733H8', 'HUTH_BACC1'))
00484         self.assertEqual(record.dr_positive[7], ('Q81AC6', 'HUTH_BACCR'))
00485         self.assertEqual(record.dr_positive[8], ('Q9KBE6', 'HUTH_BACHD'))
00486         self.assertEqual(record.dr_positive[9], ('Q6HFE9', 'HUTH_BACHK'))
00487         self.assertEqual(record.dr_positive[10], ('Q5WAZ6', 'HUTH_BACSK'))
00488         self.assertEqual(record.dr_positive[11], ('P10944', 'HUTH_BACSU'))
00489         self.assertEqual(record.dr_positive[12], ('Q6G3U8', 'HUTH_BARHE'))
00490         self.assertEqual(record.dr_positive[13], ('Q6FZP9', 'HUTH_BARQU'))
00491         self.assertEqual(record.dr_positive[14], ('Q89GV3', 'HUTH_BRAJA'))
00492         self.assertEqual(record.dr_positive[15], ('Q579E8', 'HUTH_BRUAB'))
00493         self.assertEqual(record.dr_positive[16], ('Q8FVB4', 'HUTH_BRUSU'))
00494         self.assertEqual(record.dr_positive[17], ('Q62LJ6', 'HUTH_BURMA'))
00495         self.assertEqual(record.dr_positive[18], ('Q63SH6', 'HUTH_BURPS'))
00496         self.assertEqual(record.dr_positive[19], ('Q20502', 'HUTH_CAEEL'))
00497         self.assertEqual(record.dr_positive[20], ('P58082', 'HUTH_CAUCR'))
00498         self.assertEqual(record.dr_positive[21], ('Q7P188', 'HUTH_CHRVO'))
00499         self.assertEqual(record.dr_positive[22], ('Q891Q1', 'HUTH_CLOTE'))
00500         self.assertEqual(record.dr_positive[23], ('Q9RZ06', 'HUTH_DEIRA'))
00501         self.assertEqual(record.dr_positive[24], ('Q6AKP3', 'HUTH_DESPS'))
00502         self.assertEqual(record.dr_positive[25], ('Q5L310', 'HUTH_GEOKA'))
00503         self.assertEqual(record.dr_positive[26], ('Q7NCB3', 'HUTH_GLOVI'))
00504         self.assertEqual(record.dr_positive[27], ('Q5FRR8', 'HUTH_GLUOX'))
00505         self.assertEqual(record.dr_positive[28], ('Q9HQD5', 'HUTH_HALSA'))
00506         self.assertEqual(record.dr_positive[29], ('P42357', 'HUTH_HUMAN'))
00507         self.assertEqual(record.dr_positive[30], ('Q5QV30', 'HUTH_IDILO'))
00508         self.assertEqual(record.dr_positive[31], ('Q5X5I5', 'HUTH_LEGPA'))
00509         self.assertEqual(record.dr_positive[32], ('Q5ZVR0', 'HUTH_LEGPH'))
00510         self.assertEqual(record.dr_positive[33], ('Q5WWW8', 'HUTH_LEGPL'))
00511         self.assertEqual(record.dr_positive[34], ('P35492', 'HUTH_MOUSE'))
00512         self.assertEqual(record.dr_positive[35], ('Q7N296', 'HUTH_PHOLL'))
00513         self.assertEqual(record.dr_positive[36], ('Q6LQ56', 'HUTH_PHOPR'))
00514         self.assertEqual(record.dr_positive[37], ('Q9HU85', 'HUTH_PSEAE'))
00515         self.assertEqual(record.dr_positive[38], ('Q8VMR3', 'HUTH_PSEFL'))
00516         self.assertEqual(record.dr_positive[39], ('Q88CZ7', 'HUTH_PSEPK'))
00517         self.assertEqual(record.dr_positive[40], ('P21310', 'HUTH_PSEPU'))
00518         self.assertEqual(record.dr_positive[41], ('Q87UM1', 'HUTH_PSESM'))
00519         self.assertEqual(record.dr_positive[42], ('Q8XW29', 'HUTH_RALSO'))
00520         self.assertEqual(record.dr_positive[43], ('P21213', 'HUTH_RAT'))
00521         self.assertEqual(record.dr_positive[44], ('Q983I0', 'HUTH_RHILO'))
00522         self.assertEqual(record.dr_positive[45], ('O31197', 'HUTH_RHIME'))
00523         self.assertEqual(record.dr_positive[46], ('Q57RG6', 'HUTH_SALCH'))
00524         self.assertEqual(record.dr_positive[47], ('Q5PG61', 'HUTH_SALPA'))
00525         self.assertEqual(record.dr_positive[48], ('Q8Z896', 'HUTH_SALTI'))
00526         self.assertEqual(record.dr_positive[49], ('Q8ZQQ9', 'HUTH_SALTY'))
00527         self.assertEqual(record.dr_positive[50], ('Q5LRD8', 'HUTH_SILPO'))
00528         self.assertEqual(record.dr_positive[51], ('Q5HJY8', 'HUTH_STAAC'))
00529         self.assertEqual(record.dr_positive[52], ('P64415', 'HUTH_STAAM'))
00530         self.assertEqual(record.dr_positive[53], ('P64416', 'HUTH_STAAN'))
00531         self.assertEqual(record.dr_positive[54], ('Q6GKT7', 'HUTH_STAAR'))
00532         self.assertEqual(record.dr_positive[55], ('Q6GD82', 'HUTH_STAAS'))
00533         self.assertEqual(record.dr_positive[56], ('Q8NYY3', 'HUTH_STAAW'))
00534         self.assertEqual(record.dr_positive[57], ('Q93TX3', 'HUTH_STIAU'))
00535         self.assertEqual(record.dr_positive[58], ('Q82I33', 'HUTH_STRAW'))
00536         self.assertEqual(record.dr_positive[59], ('Q9EWW1', 'HUTH_STRCO'))
00537         self.assertEqual(record.dr_positive[60], ('P24221', 'HUTH_STRGR'))
00538         self.assertEqual(record.dr_positive[61], ('P58083', 'HUTH_STRP1'))
00539         self.assertEqual(record.dr_positive[62], ('Q8K5L5', 'HUTH_STRP3'))
00540         self.assertEqual(record.dr_positive[63], ('Q5X9K4', 'HUTH_STRP6'))
00541         self.assertEqual(record.dr_positive[64], ('Q8NZ46', 'HUTH_STRP8'))
00542         self.assertEqual(record.dr_positive[65], ('Q67JH4', 'HUTH_SYMTH'))
00543         self.assertEqual(record.dr_positive[66], ('Q9HLI6', 'HUTH_THEAC'))
00544         self.assertEqual(record.dr_positive[67], ('Q8RBH4', 'HUTH_THETN'))
00545         self.assertEqual(record.dr_positive[68], ('Q978N8', 'HUTH_THEVO'))
00546         self.assertEqual(record.dr_positive[69], ('Q9KSQ4', 'HUTH_VIBCH'))
00547         self.assertEqual(record.dr_positive[70], ('Q5E0C6', 'HUTH_VIBF1'))
00548         self.assertEqual(record.dr_positive[71], ('Q87Q77', 'HUTH_VIBPA'))
00549         self.assertEqual(record.dr_positive[72], ('Q8DA21', 'HUTH_VIBVU'))
00550         self.assertEqual(record.dr_positive[73], ('Q7MK58', 'HUTH_VIBVY'))
00551         self.assertEqual(record.dr_positive[74], ('Q8PLZ8', 'HUTH_XANAC'))
00552         self.assertEqual(record.dr_positive[75], ('Q8PAA7', 'HUTH_XANCP'))
00553         self.assertEqual(record.dr_positive[76], ('Q8ZA10', 'HUTH_YERPE'))
00554         self.assertEqual(record.dr_positive[77], ('Q664B8', 'HUTH_YERPS'))
00555         self.assertEqual(record.dr_positive[78], ('Q8YD09', 'HUTIH_BRUME'))
00556         self.assertEqual(record.dr_positive[79], ('P35510', 'PAL1_ARATH'))
00557         self.assertEqual(record.dr_positive[80], ('O23865', 'PAL1_DAUCA'))
00558         self.assertEqual(record.dr_positive[81], ('P14166', 'PAL1_IPOBA'))
00559         self.assertEqual(record.dr_positive[82], ('O49835', 'PAL1_LITER'))
00560         self.assertEqual(record.dr_positive[83], ('P35511', 'PAL1_LYCES'))
00561         self.assertEqual(record.dr_positive[84], ('P14717', 'PAL1_ORYSA'))
00562         self.assertEqual(record.dr_positive[85], ('Q01861', 'PAL1_PEA'))
00563         self.assertEqual(record.dr_positive[86], ('P24481', 'PAL1_PETCR'))
00564         self.assertEqual(record.dr_positive[87], ('P45731', 'PAL1_POPKI'))
00565         self.assertEqual(record.dr_positive[88], ('O64963', 'PAL1_PRUAV'))
00566         self.assertEqual(record.dr_positive[89], ('Q9M568', 'PAL1_RUBID'))
00567         self.assertEqual(record.dr_positive[90], ('P31425', 'PAL1_SOLTU'))
00568         self.assertEqual(record.dr_positive[91], ('P27991', 'PAL1_SOYBN'))
00569         self.assertEqual(record.dr_positive[92], ('P25872', 'PAL1_TOBAC'))
00570         self.assertEqual(record.dr_positive[93], ('P45724', 'PAL2_ARATH'))
00571         self.assertEqual(record.dr_positive[94], ('Q9SMK9', 'PAL2_CICAR'))
00572         self.assertEqual(record.dr_positive[95], ('Q42858', 'PAL2_IPOBA'))
00573         self.assertEqual(record.dr_positive[96], ('O49836', 'PAL2_LITER'))
00574         self.assertEqual(record.dr_positive[97], ('P53443', 'PAL2_ORYSA'))
00575         self.assertEqual(record.dr_positive[98], ('Q04593', 'PAL2_PEA'))
00576         self.assertEqual(record.dr_positive[99], ('P45728', 'PAL2_PETCR'))
00577         self.assertEqual(record.dr_positive[100], ('P19142', 'PAL2_PHAVU'))
00578         self.assertEqual(record.dr_positive[101], ('Q43052', 'PAL2_POPKI'))
00579         self.assertEqual(record.dr_positive[102], ('P31426', 'PAL2_SOLTU'))
00580         self.assertEqual(record.dr_positive[103], ('P35513', 'PAL2_TOBAC'))
00581         self.assertEqual(record.dr_positive[104], ('P45725', 'PAL3_ARATH'))
00582         self.assertEqual(record.dr_positive[105], ('P45729', 'PAL3_PETCR'))
00583         self.assertEqual(record.dr_positive[106], ('P19143', 'PAL3_PHAVU'))
00584         self.assertEqual(record.dr_positive[107], ('P45733', 'PAL3_TOBAC'))
00585         self.assertEqual(record.dr_positive[108], ('Q9SS45', 'PAL4_ARATH'))
00586         self.assertEqual(record.dr_positive[109], ('Q40910', 'PAL4_POPKI'))
00587         self.assertEqual(record.dr_positive[110], ('P26600', 'PAL5_LYCES'))
00588         self.assertEqual(record.dr_positive[111], ('O93967', 'PALY_AMAMU'))
00589         self.assertEqual(record.dr_positive[112], ('Q42609', 'PALY_BROFI'))
00590         self.assertEqual(record.dr_positive[113], ('P45726', 'PALY_CAMSI'))
00591         self.assertEqual(record.dr_positive[114], ('Q42667', 'PALY_CITLI'))
00592         self.assertEqual(record.dr_positive[115], ('O23924', 'PALY_DIGLA'))
00593         self.assertEqual(record.dr_positive[116], ('O04058', 'PALY_HELAN'))
00594         self.assertEqual(record.dr_positive[117], ('P27990', 'PALY_MEDSA'))
00595         self.assertEqual(record.dr_positive[118], ('P45727', 'PALY_PERAE'))
00596         self.assertEqual(record.dr_positive[119], ('P52777', 'PALY_PINTA'))
00597         self.assertEqual(record.dr_positive[120], ('P45730', 'PALY_POPTR'))
00598         self.assertEqual(record.dr_positive[121], ('P10248', 'PALY_RHORB'))
00599         self.assertEqual(record.dr_positive[122], ('P11544', 'PALY_RHOTO'))
00600         self.assertEqual(record.dr_positive[123], ('P45732', 'PALY_STYHU'))
00601         self.assertEqual(record.dr_positive[124], ('P45734', 'PALY_TRISU'))
00602         self.assertEqual(record.dr_positive[125], ('Q96V77', 'PALY_USTMA'))
00603         self.assertEqual(record.dr_positive[126], ('Q43210', 'PALY_WHEAT'))
00604         self.assertEqual(len(record.dr_false_neg), 2)
00605         self.assertEqual(record.dr_false_neg[0], ('Q8EKJ4', 'HUTH_SHEON'))
00606         self.assertEqual(record.dr_false_neg[1], ('Q73Q56', 'HUTH_TREDE'))
00607         self.assertEqual(len(record.dr_false_pos), 0)
00608         self.assertEqual(len(record.dr_potential), 4)
00609         self.assertEqual(record.dr_potential[0], ('P07218', 'PAL1_PHAVU'))
00610         self.assertEqual(record.dr_potential[1], ('Q92195', 'PALY_AGABI'))
00611         self.assertEqual(record.dr_potential[2], ('P35512', 'PALY_MALDO'))
00612         self.assertEqual(record.dr_potential[3], ('P45735', 'PALY_VITVI'))
00613         self.assertEqual(len(record.dr_unknown), 0)
00614         self.assertEqual(record.pdb_structs[0], "1B8F")
00615         self.assertEqual(record.pdb_structs[1], "1EB4")
00616         self.assertEqual(record.pdb_structs[2], "1GK2")
00617         self.assertEqual(record.pdb_structs[3], "1GKJ")
00618         self.assertEqual(record.pdb_structs[4], "1GKM")
00619         self.assertEqual(record.pdb_structs[5], "1Y2M")

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Definition at line 620 of file test_prosite2.py.

00620 
00621     def test_read6(self):
00622         "Parsing Prosite record ps00546.txt"
00623         filename = os.path.join('Prosite', 'ps00546.txt')
00624         handle = open(filename)
00625         record = Prosite.read(handle)
00626         self.assertEqual(record.name, "CYSTEINE_SWITCH")
00627         self.assertEqual(record.type, "PATTERN")
00628         self.assertEqual(record.accession, "PS00546")
00629         self.assertEqual(record.created, "DEC-1991")
00630         self.assertEqual(record.data_update, "NOV-1997")
00631         self.assertEqual(record.info_update, "MAR-2006")
00632         self.assertEqual(record.pdoc, "PDOC00472")
00633         self.assertEqual(record.description, "Matrixins cysteine switch.")
00634         self.assertEqual(record.pattern, "P-R-C-[GN]-x-P-[DR]-[LIVSAPKQ].")
00635         self.assertEqual(record.matrix, [])
00636         self.assertEqual(record.rules, [])
00637         self.assertEqual(record.nr_sp_release, "49.3")
00638         self.assertEqual(record.nr_sp_seqs, 212425)
00639         self.assertEqual(record.cc_taxo_range, "??E??")
00640         self.assertEqual(record.cc_max_repeat, "1")
00641         self.assertEqual(len(record.cc_site), 1)
00642         self.assertEqual(record.cc_site[0], (3, 'chelates_zinc'))
00643         self.assertEqual(len(record.dr_positive), 62)
00644         self.assertEqual(record.dr_positive[0], ('P31178', 'GLE_CHLRE'))
00645         self.assertEqual(record.dr_positive[1], ('P91953', 'HE_HEMPU'))
00646         self.assertEqual(record.dr_positive[2], ('P22757', 'HE_PARLI'))
00647         self.assertEqual(record.dr_positive[3], ('P29136', 'MEP1_SOYBN'))
00648         self.assertEqual(record.dr_positive[4], ('P09238', 'MMP10_HUMAN'))
00649         self.assertEqual(record.dr_positive[5], ('O55123', 'MMP10_MOUSE'))
00650         self.assertEqual(record.dr_positive[6], ('P07152', 'MMP10_RAT'))
00651         self.assertEqual(record.dr_positive[7], ('P24347', 'MMP11_HUMAN'))
00652         self.assertEqual(record.dr_positive[8], ('Q11005', 'MMP11_XENLA'))
00653         self.assertEqual(record.dr_positive[9], ('P39900', 'MMP12_HUMAN'))
00654         self.assertEqual(record.dr_positive[10], ('P34960', 'MMP12_MOUSE'))
00655         self.assertEqual(record.dr_positive[11], ('P79227', 'MMP12_RABIT'))
00656         self.assertEqual(record.dr_positive[12], ('O77656', 'MMP13_BOVIN'))
00657         self.assertEqual(record.dr_positive[13], ('O18927', 'MMP13_HORSE'))
00658         self.assertEqual(record.dr_positive[14], ('P45452', 'MMP13_HUMAN'))
00659         self.assertEqual(record.dr_positive[15], ('P33435', 'MMP13_MOUSE'))
00660         self.assertEqual(record.dr_positive[16], ('O62806', 'MMP13_RABIT'))
00661         self.assertEqual(record.dr_positive[17], ('P23097', 'MMP13_RAT'))
00662         self.assertEqual(record.dr_positive[18], ('Q10835', 'MMP13_XENLA'))
00663         self.assertEqual(record.dr_positive[19], ('P50281', 'MMP14_HUMAN'))
00664         self.assertEqual(record.dr_positive[20], ('P53690', 'MMP14_MOUSE'))
00665         self.assertEqual(record.dr_positive[21], ('Q9XT90', 'MMP14_PIG'))
00666         self.assertEqual(record.dr_positive[22], ('Q95220', 'MMP14_RABIT'))
00667         self.assertEqual(record.dr_positive[23], ('Q10739', 'MMP14_RAT'))
00668         self.assertEqual(record.dr_positive[24], ('P51511', 'MMP15_HUMAN'))
00669         self.assertEqual(record.dr_positive[25], ('O54732', 'MMP15_MOUSE'))
00670         self.assertEqual(record.dr_positive[26], ('P51512', 'MMP16_HUMAN'))
00671         self.assertEqual(record.dr_positive[27], ('Q9WTR0', 'MMP16_MOUSE'))
00672         self.assertEqual(record.dr_positive[28], ('O35548', 'MMP16_RAT'))
00673         self.assertEqual(record.dr_positive[29], ('Q9EPL5', 'MMP1A_MOUSE'))
00674         self.assertEqual(record.dr_positive[30], ('Q9EPL6', 'MMP1B_MOUSE'))
00675         self.assertEqual(record.dr_positive[31], ('P28053', 'MMP1_BOVIN'))
00676         self.assertEqual(record.dr_positive[32], ('Q9XSZ5', 'MMP1_HORSE'))
00677         self.assertEqual(record.dr_positive[33], ('P03956', 'MMP1_HUMAN'))
00678         self.assertEqual(record.dr_positive[34], ('P21692', 'MMP1_PIG'))
00679         self.assertEqual(record.dr_positive[35], ('P13943', 'MMP1_RABIT'))
00680         self.assertEqual(record.dr_positive[36], ('O18767', 'MMP20_BOVIN'))
00681         self.assertEqual(record.dr_positive[37], ('O60882', 'MMP20_HUMAN'))
00682         self.assertEqual(record.dr_positive[38], ('P57748', 'MMP20_MOUSE'))
00683         self.assertEqual(record.dr_positive[39], ('P79287', 'MMP20_PIG'))
00684         self.assertEqual(record.dr_positive[40], ('Q90611', 'MMP2_CHICK'))
00685         self.assertEqual(record.dr_positive[41], ('P08253', 'MMP2_HUMAN'))
00686         self.assertEqual(record.dr_positive[42], ('P33434', 'MMP2_MOUSE'))
00687         self.assertEqual(record.dr_positive[43], ('P50757', 'MMP2_RABIT'))
00688         self.assertEqual(record.dr_positive[44], ('P33436', 'MMP2_RAT'))
00689         self.assertEqual(record.dr_positive[45], ('Q6Y4Q5', 'MMP3_CANFA'))
00690         self.assertEqual(record.dr_positive[46], ('P08254', 'MMP3_HUMAN'))
00691         self.assertEqual(record.dr_positive[47], ('P28862', 'MMP3_MOUSE'))
00692         self.assertEqual(record.dr_positive[48], ('P28863', 'MMP3_RABIT'))
00693         self.assertEqual(record.dr_positive[49], ('P03957', 'MMP3_RAT'))
00694         self.assertEqual(record.dr_positive[50], ('P09237', 'MMP7_HUMAN'))
00695         self.assertEqual(record.dr_positive[51], ('Q10738', 'MMP7_MOUSE'))
00696         self.assertEqual(record.dr_positive[52], ('P50280', 'MMP7_RAT'))
00697         self.assertEqual(record.dr_positive[53], ('P22894', 'MMP8_HUMAN'))
00698         self.assertEqual(record.dr_positive[54], ('O70138', 'MMP8_MOUSE'))
00699         self.assertEqual(record.dr_positive[55], ('O88766', 'MMP8_RAT'))
00700         self.assertEqual(record.dr_positive[56], ('P52176', 'MMP9_BOVIN'))
00701         self.assertEqual(record.dr_positive[57], ('O18733', 'MMP9_CANFA'))
00702         self.assertEqual(record.dr_positive[58], ('P14780', 'MMP9_HUMAN'))
00703         self.assertEqual(record.dr_positive[59], ('P41245', 'MMP9_MOUSE'))
00704         self.assertEqual(record.dr_positive[60], ('P41246', 'MMP9_RABIT'))
00705         self.assertEqual(record.dr_positive[61], ('P50282', 'MMP9_RAT'))
00706         self.assertEqual(len(record.dr_false_neg), 59)
00707         self.assertEqual(record.dr_false_neg[0], ('Q9R158', 'AD26A_MOUSE'))
00708         self.assertEqual(record.dr_false_neg[1], ('Q10741', 'ADA10_BOVIN'))
00709         self.assertEqual(record.dr_false_neg[2], ('O14672', 'ADA10_HUMAN'))
00710         self.assertEqual(record.dr_false_neg[3], ('O35598', 'ADA10_MOUSE'))
00711         self.assertEqual(record.dr_false_neg[4], ('Q10743', 'ADA10_RAT'))
00712         self.assertEqual(record.dr_false_neg[5], ('Q8JIY1', 'ADA10_XENLA'))
00713         self.assertEqual(record.dr_false_neg[6], ('Q61824', 'ADA12_MOUSE'))
00714         self.assertEqual(record.dr_false_neg[7], ('Q13444', 'ADA15_HUMAN'))
00715         self.assertEqual(record.dr_false_neg[8], ('O88839', 'ADA15_MOUSE'))
00716         self.assertEqual(record.dr_false_neg[9], ('Q9QYV0', 'ADA15_RAT'))
00717         self.assertEqual(record.dr_false_neg[10], ('P78536', 'ADA17_HUMAN'))
00718         self.assertEqual(record.dr_false_neg[11], ('Q9Z0F8', 'ADA17_MOUSE'))
00719         self.assertEqual(record.dr_false_neg[12], ('Q9Z1K9', 'ADA17_RAT'))
00720         self.assertEqual(record.dr_false_neg[13], ('Q9H013', 'ADA19_HUMAN'))
00721         self.assertEqual(record.dr_false_neg[14], ('O35674', 'ADA19_MOUSE'))
00722         self.assertEqual(record.dr_false_neg[15], ('O43506', 'ADA20_HUMAN'))
00723         self.assertEqual(record.dr_false_neg[16], ('Q9UKJ8', 'ADA21_HUMAN'))
00724         self.assertEqual(record.dr_false_neg[17], ('Q9JI76', 'ADA21_MOUSE'))
00725         self.assertEqual(record.dr_false_neg[18], ('Q9R160', 'ADA24_MOUSE'))
00726         self.assertEqual(record.dr_false_neg[19], ('Q9R159', 'ADA25_MOUSE'))
00727         self.assertEqual(record.dr_false_neg[20], ('Q9UKQ2', 'ADA28_HUMAN'))
00728         self.assertEqual(record.dr_false_neg[21], ('Q9XSL6', 'ADA28_MACFA'))
00729         self.assertEqual(record.dr_false_neg[22], ('Q9JLN6', 'ADA28_MOUSE'))
00730         self.assertEqual(record.dr_false_neg[23], ('Q9UKF2', 'ADA30_HUMAN'))
00731         self.assertEqual(record.dr_false_neg[24], ('Q9BZ11', 'ADA33_HUMAN'))
00732         self.assertEqual(record.dr_false_neg[25], ('Q923W9', 'ADA33_MOUSE'))
00733         self.assertEqual(record.dr_false_neg[26], ('O15204', 'ADEC1_HUMAN'))
00734         self.assertEqual(record.dr_false_neg[27], ('P58397', 'ATS12_HUMAN'))
00735         self.assertEqual(record.dr_false_neg[28], ('Q811B3', 'ATS12_MOUSE'))
00736         self.assertEqual(record.dr_false_neg[29], ('Q8WXS8', 'ATS14_HUMAN'))
00737         self.assertEqual(record.dr_false_neg[30], ('Q8TE58', 'ATS15_HUMAN'))
00738         self.assertEqual(record.dr_false_neg[31], ('P59384', 'ATS15_MOUSE'))
00739         self.assertEqual(record.dr_false_neg[32], ('Q8TE57', 'ATS16_HUMAN'))
00740         self.assertEqual(record.dr_false_neg[33], ('Q69Z28', 'ATS16_MOUSE'))
00741         self.assertEqual(record.dr_false_neg[34], ('Q8TE56', 'ATS17_HUMAN'))
00742         self.assertEqual(record.dr_false_neg[35], ('Q8TE60', 'ATS18_HUMAN'))
00743         self.assertEqual(record.dr_false_neg[36], ('Q4VC17', 'ATS18_MOUSE'))
00744         self.assertEqual(record.dr_false_neg[37], ('Q8TE59', 'ATS19_HUMAN'))
00745         self.assertEqual(record.dr_false_neg[38], ('P59509', 'ATS19_MOUSE'))
00746         self.assertEqual(record.dr_false_neg[39], ('Q9UKP4', 'ATS7_HUMAN'))
00747         self.assertEqual(record.dr_false_neg[40], ('Q9P2N4', 'ATS9_HUMAN'))
00748         self.assertEqual(record.dr_false_neg[41], ('Q02853', 'MMP11_MOUSE'))
00749         self.assertEqual(record.dr_false_neg[42], ('Q63341', 'MMP12_RAT'))
00750         self.assertEqual(record.dr_false_neg[43], ('Q9ULZ9', 'MMP17_HUMAN'))
00751         self.assertEqual(record.dr_false_neg[44], ('Q9R0S3', 'MMP17_MOUSE'))
00752         self.assertEqual(record.dr_false_neg[45], ('O13065', 'MMP18_XENLA'))
00753         self.assertEqual(record.dr_false_neg[46], ('Q99542', 'MMP19_HUMAN'))
00754         self.assertEqual(record.dr_false_neg[47], ('Q9JHI0', 'MMP19_MOUSE'))
00755         self.assertEqual(record.dr_false_neg[48], ('Q11133', 'MMP1_RANCA'))
00756         self.assertEqual(record.dr_false_neg[49], ('Q90YC2', 'MMP21_CYNPY'))
00757         self.assertEqual(record.dr_false_neg[50], ('Q8N119', 'MMP21_HUMAN'))
00758         self.assertEqual(record.dr_false_neg[51], ('Q8K3F2', 'MMP21_MOUSE'))
00759         self.assertEqual(record.dr_false_neg[52], ('O93470', 'MMP21_XENLA'))
00760         self.assertEqual(record.dr_false_neg[53], ('Q9Y5R2', 'MMP24_HUMAN'))
00761         self.assertEqual(record.dr_false_neg[54], ('Q9R0S2', 'MMP24_MOUSE'))
00762         self.assertEqual(record.dr_false_neg[55], ('Q9NRE1', 'MMP26_HUMAN'))
00763         self.assertEqual(record.dr_false_neg[56], ('Q9H239', 'MMP28_HUMAN'))
00764         self.assertEqual(record.dr_false_neg[57], ('Q28397', 'MMP3_HORSE'))
00765         self.assertEqual(record.dr_false_neg[58], ('P55032', 'MMP7_FELCA'))
00766         self.assertEqual(len(record.dr_false_pos), 1)
00767         self.assertEqual(record.dr_false_pos[0], ('Q9YC75', 'RGYR2_AERPE'))
00768         self.assertEqual(len(record.dr_potential), 0)
00769         self.assertEqual(len(record.dr_unknown), 0)
00770         self.assertEqual(len(record.pdb_structs), 8)
00771         self.assertEqual(record.pdb_structs[0], "1CK7")
00772         self.assertEqual(record.pdb_structs[1], "1EAK")
00773         self.assertEqual(record.pdb_structs[2], "1GXD")
00774         self.assertEqual(record.pdb_structs[3], "1L6J")
00775         self.assertEqual(record.pdb_structs[4], "1LKG")
00776         self.assertEqual(record.pdb_structs[5], "1SLM")
00777         self.assertEqual(record.pdb_structs[6], "1SU3")
00778         self.assertEqual(record.pdb_structs[7], "1UC1")
00779 
00780 

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The documentation for this class was generated from the following file: