def actionLoadSequence(self, event=None):
filename = tkinter.filedialog.askopenfilename()
if filename:
seq = sequenceIO.readFile(filename)
self.textSourceSeq.delete("1.0", "end")
self.textSourceSeq.insert("end", seq)
self.textSourceSeq.edit_modified(True)
def actionLoadSequence(self, event=None):
filename = tkinter.filedialog.askopenfilename()
if filename:
seq = sequenceIO.readFile(filename)
self.textSourceSeq.delete("1.0", "end")
self.textSourceSeq.insert("end", seq)
self.textSourceSeq.edit_modified(True)
def main(argv):
if (len(argv) != 4):
print(
"Usage: optimize.py [sequence file] [source taxid] [target taxid]")
sys.exit()
seqfile = argv[1]
src_taxid = argv[2]
trg_taxid = argv[3]
seq = sequenceIO.readFile(seqfile)
seqr = sequenceIO.D2R(seq)
print("== INPUT SEQUENCE, GC: ", round(seqstats.getGC(seq) * 100), "%")
# print(seq)
cuSrc = kazusaIO.getCU(src_taxid)
cuTrg = kazusaIO.getCU(trg_taxid)
opt = optimizing.RelativeUsageCodonOptimizer(cuSrc, cuTrg)
inCodons = re.findall('...', seqr) # list of codons
outCodons = list()
for c in inCodons:
outCodons.append(opt.optimize(c))
for i in range(0, len(outCodons)):
if outCodons[i] == inCodons[i]:
print(sequenceIO.R2D(inCodons[i]), end="")
else:
print(bcolors.OKGREEN,
sequenceIO.R2D(inCodons[i]),
bcolors.ENDC,
end="",
sep="")
print("") #newline
res = "".join(outCodons)
resd = sequenceIO.R2D(res)
print("== OPTIMIZED SEQUENCE, GC: ", round(seqstats.getGC(resd) * 100),
"%")
for i in range(0, len(outCodons)):
if outCodons[i] == inCodons[i]:
print(sequenceIO.R2D(outCodons[i]), end="")
else:
print(bcolors.WARNING,
sequenceIO.R2D(outCodons[i]),
bcolors.ENDC,
end="",
sep="")
print("") #newline
print("== STATS: CHANGED CODONS: ",
seqstats.getChanged(seq, resd)[0], "/",
seqstats.getChanged(seq, resd)[1])
def main(argv):
if (len(argv) != 4):
print("Usage: optimize.py [sequence file] [source taxid] [target taxid]")
sys.exit()
seqfile = argv[1]
src_taxid = argv[2]
trg_taxid = argv[3]
seq = sequenceIO.readFile(seqfile)
seqr = sequenceIO.D2R(seq)
print("== INPUT SEQUENCE, GC: ", round(seqstats.getGC(seq)*100), "%")
# print(seq)
cuSrc = kazusaIO.getCU(src_taxid)
cuTrg = kazusaIO.getCU(trg_taxid)
opt = optimizing.RelativeUsageCodonOptimizer(cuSrc, cuTrg)
inCodons = re.findall('...', seqr) # list of codons
outCodons = list()
for c in inCodons:
outCodons.append(opt.optimize(c))
for i in range(0, len(outCodons)):
if outCodons[i] == inCodons[i]:
print(sequenceIO.R2D(inCodons[i]), end="")
else:
print(bcolors.OKGREEN, sequenceIO.R2D(inCodons[i]), bcolors.ENDC, end="", sep="")
print("") #newline
res = "".join(outCodons)
resd = sequenceIO.R2D(res)
print("== OPTIMIZED SEQUENCE, GC: ", round(seqstats.getGC(resd)*100), "%")
for i in range(0, len(outCodons)):
if outCodons[i] == inCodons[i]:
print(sequenceIO.R2D(outCodons[i]), end="")
else:
print(bcolors.WARNING, sequenceIO.R2D(outCodons[i]), bcolors.ENDC, end="", sep="")
print("") #newline
print("== STATS: CHANGED CODONS: ", seqstats.getChanged(seq, resd)[0], "/", seqstats.getChanged(seq, resd)[1])
