def test_history():
global pts
db = DataBase()
psmotif = "AAGSGGAAGQAASAAAGAGKGLAA"
db.AddSeq(psmotif)
for i in pts: db.AddSeq(i)
db.SMFromFile("blosum62.mat")
db.DBupgma()
#db.SearchDomains(1) #slow but works
db.ExportHistory()
db2 = DataBase()
db2.ImportHistory()
print(db2.domains)
def test_RegexInDB():
global pts
db = DataBase()
for i in pts: db.AddSeq(i)
print(db.RegexInDB("FGHI")) #list of tuples (key in db, index in seq)
print(db.RegexInDB("FGHI",1)) #list of indexes in seq
print(db.RegexInDB("E*FGHI"))
def test_FreqInDB():
global pts
db = DataBase()
for i in pts: db.AddSeq(i)
print(db.FreqInDB("FG"))
print(db.FreqInDB("FG",1))
#print(db.FreqInDB("*")) #gives error
print(db.FreqInDB("O"))
def test_SearchDomains():
psmotif = "AAGSGGAAGQAASAAAGAGKGLAA"
db = DataBase()
db.AddSeq(psmotif)
db.SearchDomains(1)
print(db.domains)
def test_SaveFile():
global pts
db = DataBase()
for i in pts: db.AddSeq(i)
db.SaveFile()
def test_DBmultiAlign():
db = DataBase()
for i in pts: db.AddSeq(i)
db.SMFromFile("blosum62.mat")
db.DBupgma()
print(db.DBmultiAlign([1,2]))
def test_Clustal():
db = DataBase()
for i in pts: db.AddSeq(i)
db.SMFromFile("blosum62.mat")
db.Clustal(path,"testfasta.txt")
def test_AddSeq():
db = DataBase()
db.AddSeq("MEIDKFVKEEDIPFEYGVVRERDNAVSWSRYL") #Valid
db.AddSeq("MEIDKFVKEE111VRERDNAVSWSRYL") #Invalid
db.AddSeq("MEIDKFVKEEDIPFEYGVVRERDNAVSWSRYL") #Repeated
for i in db.dseqs.values(): print(i.seq)
def test_SimilarInDB():
global pts
db = DataBase()
for i in pts: db.AddSeq(i)
db.SMFromFile("blosum62.mat")
print(db.SimilarInDB("ACDEFGHI"))
