예제 #1
0
파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_checkMetIns1(self):
     print("Testing checking 1 AA insertion after Met")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRX",
                                "MQLRX",
                                3,
                                strict_hgvs=True)
     expected = ('_p.Met1_Leu2insGln', ('1-2', '-', 'Q'))
     self.assertEqual(actual, expected)
예제 #2
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_del1(self):
     print("Testing deletion of 1AA")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRX",
                                "MRX",
                                1,
                                strict_hgvs=True)
     expected = ('_p.Leu2del', ('2', 'L', '-'))
     self.assertEqual(actual, expected)
예제 #3
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_extNoTer(self):
     print("Testing checking delins")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRX",
                                "MLRLVI",
                                7,
                                strict_hgvs=True)
     expected = ('_p.Ter4Leuext*?', ('4', 'X', 'LVI'))
     self.assertEqual(actual, expected)
예제 #4
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_Met1toAA(self):
     print("Testing mutation of  Methionine")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRX",
                                "LLRX",
                                1,
                                strict_hgvs=True)
     expected = ('_p.?', ('1', 'M', 'L'))
     self.assertEqual(actual, expected)
예제 #5
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_checkLongFS(self):
     print("Testing checking long frameshift")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRYQVQX",
                                "MLQYLVMSNX",
                                7,
                                strict_hgvs=True)
     expected = ('_p.Arg3GlnfsTer8', ('3', 'R', 'QYLVMSNX'))
     self.assertEqual(actual, expected)
예제 #6
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_checkDellookLikeShortFS(self):
     print("Testing checking Deletion")
     variant = Variant("chr1", 1000, "CTGGCTTCGGTCG", "C")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRYQVQX",
                                "MLQX",
                                7,
                                strict_hgvs=True)
     expected = ('_p.Arg3_Val6del', ('3-6', 'RYQV', '-'))
     self.assertEqual(actual, expected)
예제 #7
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_checkDelasFS(self):
     print("Testing checking check frameshift")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRYQVRX",
                                "MLRVX",
                                6,
                                strict_hgvs=True)
     expected = ('_p.Tyr4ValfsTer2', ('4', 'Y', 'VX'))
     self.assertEqual(actual, expected)
예제 #8
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_checkShortFS(self):
     print("Testing checking frameshift with mutprot<prot")
     variant = Variant("chr1", 1000, "CT", "C")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRYQVRX",
                                "MLSVX",
                                8,
                                strict_hgvs=True)
     expected = ('_p.Arg3SerfsTer3', ('3', 'R', 'SVX'))
     self.assertEqual(actual, expected)
예제 #9
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_checkLongExtnotPhase(self):
     print("Testing checking long extension not in phase")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRX",
                                "MLRQLVYX",
                                11,
                                strict_hgvs=True)
     expected = ('_p.Ter4GlnextX5', ('4', 'X', 'QLVYX'))
     self.assertEqual(actual, expected)
예제 #10
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_Syn(self):
     variant = Variant("chr1", 1000, "C", "T")
     #        print("Testing Syn Change\n")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MRX",
                                "MLX",
                                6,
                                strict_hgvs=True)
     expected = ('_p.Arg2Leu', ('2', 'R', 'L'))
     self.assertEqual(actual, expected)
예제 #11
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_delins(self):
     print("Testing checking delins")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRYQVQX",
                                "MLRLVISVQX",
                                7,
                                strict_hgvs=True)
     expected = ('_p.Tyr4_Gln5delinsLeuValIleSer', ('4-5', 'YQ', 'LVIS'))
     self.assertEqual(actual, expected)
예제 #12
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_dup_AA(self):
     print("Testing checking dup of pattern 2 AA long")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLYRX",
                                "MLYLYRX",
                                6,
                                strict_hgvs=True)
     expected = ('_p.Leu2_Tyr3dup', ('3-4', '-', 'LY'))
     self.assertEqual(actual, expected)
예제 #13
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_Met1toAAS(self):
     print("Testing mutation of  2 AA (including Methionine)")
     variant = Variant("chr1", 1000, "CTCT", "TCAG")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRX",
                                "LRRX",
                                1,
                                strict_hgvs=True)
     expected = ('_p.?', ('1-2', 'ML', 'LR'))
     self.assertEqual(actual, expected)
예제 #14
0
파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinStringf_ssr1_loss2to1(self):
     print("Testing checking ssr 2-long deletion")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLLRX",
                                "MLRX",
                                6,
                                strict_hgvs=True)
     expected = ('_p.Leu2[2]%3B[1]', ('3', 'L', '-'))
     self.assertEqual(actual, expected)
예제 #15
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_EarlyStopInMiddleOutofPhase(self):
     variant = Variant("chr1", 1000, "C", "T")
     print("Early Stop - 3rd pos of 6\n")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MYLRGX",
                                "MYX",
                                8,
                                strict_hgvs=True)
     expected = ('_p.Leu3Ter', ('3', 'L', 'X'))
     self.assertEqual(actual, expected)
예제 #16
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_EarlyStopNearEnd(self):
     variant = Variant("chr1", 1000, "C", "T")
     print("Early Stop - 2nd pos of 3\n")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MRX",
                                "MX",
                                4,
                                strict_hgvs=True)
     expected = ('_p.Arg2Ter', ('2', 'R', 'X'))
     self.assertEqual(actual, expected)
예제 #17
0
파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_ssr2_loss2to0(self):
     print("Testing checking ssr 2-long deletion to 0")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLYLYRX",
                                "MRX",
                                6,
                                strict_hgvs=True)
     expected = ('_p.Leu2_Tyr3[2]%3B[0]', ('2-5', 'LYLY', '-'))
     self.assertEqual(actual, expected)
예제 #18
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_ssr2_gain1to3(self):
     print("Testing checking ssr 1 to 3 copies of 2-long SSR")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLYRX",
                                "MLYLYLYRX",
                                6,
                                strict_hgvs=True)
     expected = ('_p.Leu2_Tyr3[1]%3B[3]', ('3-4', '-', 'LYLY'))
     self.assertEqual(actual, expected)
예제 #19
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_delMet1(self):
     print("Testing deletion of Initial Methionine")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRX",
                                "LRX",
                                1,
                                strict_hgvs=True)
     expected = ('_p.?', ('1', 'M', '-'))
     self.assertEqual(actual, expected)
예제 #20
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_checkShortExt(self):
     print("Testing checking extension")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRX",
                                "MLRQX",
                                12,
                                strict_hgvs=True)
     expected = ('_p.Ter4GlnextX2', ('4', 'X', 'QX'))
     self.assertEqual(actual, expected)
예제 #21
0
파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_dup1(self):
     print("Testing checking dup of 1 base")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRX",
                                "MLLRX",
                                6,
                                strict_hgvs=True)
     expected = ('_p.Leu2dup', ('2-3', '-', 'L'))
     self.assertEqual(actual, expected)
예제 #22
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_del2(self):
     print("Testing deletion 2AA")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRYX",
                                "MYX",
                                1,
                                strict_hgvs=True)
     expected = ('_p.Leu2_Arg3del', ('2-3', 'LR', '-'))
     self.assertEqual(actual, expected)
예제 #23
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_emptyProt(self):
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "",
                                "MLX",
                                1,
                                strict_hgvs=True)
     expected = ('', ('.', '.', '.'))
     print("Testing prot= empty\n")
     self.assertEqual(actual, expected)
예제 #24
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_ssr1_gain1to3(self):
     print("Testing checking 1 to 3 copies of 1-long SSR")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRX",
                                "MLLLRX",
                                6,
                                strict_hgvs=True)
     expected = ('_p.Leu2[1]%3B[3]', ('2-3', '-', 'LL'))
     self.assertEqual(actual, expected)
예제 #25
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_EarlyStopInMiddle3BP(
         self):  # Note variant is not being used.. just possibly frame
     variant = Variant("chr1", 1000, "C", "TTCA")
     print("Early Stop - 3rd pos of 6, from in phase insertion\n")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MYLRGX",
                                "MYX",
                                9,
                                strict_hgvs=True)
     expected = ('_p.Leu3Ter', ('3', 'L', 'X'))
     self.assertEqual(actual, expected)
예제 #26
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_delinsasFS(self):
     print("Testing checking delins affecting Stop Should be an FS ")
     variant = Variant("chr1", 1000, "C", "T")
     # Q --> LXR
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRYQX",
                                "MLRLRX",
                                7,
                                strict_hgvs=True)
     expected = ('_p.Tyr4LeufsTer3', ('4', 'Y', 'LRX'))
     self.assertEqual(actual, expected)
예제 #27
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_checkInsTer(self):
     print(
         "Testing checking 3AA Insertion that contains a Ter in the middle")
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRQX",
                                "MLLXLRQX",
                                3,
                                strict_hgvs=True)
     expected = ('_p.Leu2_Arg3insLeuTer', ('2-3', '-', 'LX'))
     self.assertEqual(actual, expected)
예제 #28
0
파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_delinswithTerAsFS(self):
     print("Testing checking delins 1 AA becoming 3 (with Ter in middle) ")
     variant = Variant("chr1", 1000, "C", "T")
     # Q --> LXR
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MLRYQVQX",
                                "MLRYLXRVQX",
                                7,
                                strict_hgvs=True)
     expected = ('_p.Gln5delinsLeuTer', ('5', 'Q', 'LX'))
     self.assertEqual(actual, expected)
예제 #29
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파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_basic(self):
     print("Testing checking basic change")
     variant = Variant("chr17", 43045712, "T", "C")
     REF = "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPENPSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEISLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENSSLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPCSENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLLASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKRKRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEKESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSEEIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKEFVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLGKAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVSKRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKDKPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRPPLFPIKSFVKTKCKKNLLEENFEEHSMSPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKLNAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDDLLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELPCFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLFSSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEAASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALEDLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHSCSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRAPESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSGLTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKMLNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY"
     ALT = "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPENPSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEISLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENSSLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPCSENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLLASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKRKRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEKESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSEEIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKEFVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLGKAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVSKRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKDKPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRPPLFPIKSFVKTKCKKNLLEENFEEHSMSPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKLNAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDDLLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELPCFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLFSSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEAASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALEDLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHSCSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRAPESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSGLTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKMLNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTLGTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTCLIPQIPHSHY"
     actual = makeProteinString(variant,
                                "ENST00000357654.9",
                                "chr17",
                                REF,
                                ALT,
                                5558,
                                strict_hgvs=True)
     expected = ('_p.Tyr1852Cys', ('1852', 'Y', 'C'))
     self.assertEqual(actual, expected)
예제 #30
0
파일: test_csn.py 프로젝트: sicotteh/CAVA
 def test_makeProteinString_ssr2_gain0to3(self):
     print(
         "Testing checking ssr 0 to 3 copies of 2-long SSR .. should not be an SSR"
     )
     variant = Variant("chr1", 1000, "C", "T")
     actual = makeProteinString(variant,
                                "NM",
                                "chr1",
                                "MRX",
                                "MLYLYLYRX",
                                6,
                                strict_hgvs=True)
     expected = ('_p.Met1_Arg2insLeuTyrLeuTyrLeuTyr', ('1-2', '-',
                                                       'LYLYLY'))
     self.assertEqual(actual, expected)