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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)