def test_args(self):
result = color("red bold")
self.assertEqual(result, "\033[31;1m")
result = color("red, bold")
self.assertEqual(result, "\033[31;1m")
result = color(["red", "bold"])
self.assertEqual(result, "\033[31;1m")
def printReadingFrames(num, compStrandDNA, mRNA, protein, metStart, metIn,
stopEnd, stopIn):
# param num: reading frame number
# param compStrandDNA: DNA template strand (matching gene of interest)
# param compStrandmRNA: mRNA complement strand (matching gene of interest)
# param protein: amino acids of gene of interest
# param metStart: Met at the start of gene
# param metIn: Met in gene
# param stopEnd: stop codon at the end of gene
# param stopIn: stop codon in gene
# type num: integer
# type compStrandDNA: string
# type mRNA: string
# type protein: string
# type metStart: boolean
# type metIn: boolean
# type stopEnd: boolean
# type stopIn: boolean
read = ""
# beginning of reading frame
read += "Reading Frame #{}\n".format(num)
read += "RNA length: %i\n" % len(compStrandDNA)
# add color to mRNA
mRNAList = list(mRNA)
for letter in mRNAList:
letterIndex = mRNAList.index(letter)
if letter == "A":
mRNAList[letterIndex] = color('cyan') + letter + color('reset')
elif letter == "U":
mRNAList[letterIndex] = color('blue') + letter + color('reset')
elif letter == "C":
mRNAList[letterIndex] = color('bold red') + letter + color('reset')
elif letter == "G":
mRNAList[letterIndex] = color('bold magenta') + letter + color(
'reset')
mRNA = ''.join(mRNAList)
# continued beginning
read += "\tRNA:\t\t%s\n" % mRNA
lines = "| " * (len(compStrandDNA) // 3)
read += "\t\t\t\t %s\n" % lines
read += "\tProtein:\t%s\n\n" % protein
# summary for Met at start
if metStart == True:
read += "There is a Met at the start site.\n"
else:
read += "There is no Met at the start site.\n"
# summary for stop at end
if stopEnd == True:
read += "There is a stop at the end.\n"
else:
read += "There is no stop at the end.\n"
# summary for Met inside strand
if metIn == True:
read += "There is at least one Met somewhere other than at the start.\n"
else:
read += "There are no Mets other than at the start.\n"
# summary for stop inside strand
if stopIn == True:
read += "There is at least one stop interrupting the gene."
else:
read += "There are no interrupting stops."
return read
def test_env(self):
with patch.dict("os.environ", {"ANSI_COLORS_DISABLED": "1"}):
result = color("red")
self.assertEqual(result, "")
def test_arg(self):
result = color("red")
self.assertEqual(result, "\033[31m")
def test_bad(self):
with self.assertRaisesRegex(ValueError, r"invalid attribute name.*"):
color("infrared")
def printReadingFrames(num, compStrandDNA, mRNA, protein, metStart, metIn, stopEnd, stopIn):
# param num: reading frame number
# param compStrandDNA: DNA template strand (matching gene of interest)
# param compStrandmRNA: mRNA complement strand (matching gene of interest)
# param protein: amino acids of gene of interest
# param metStart: Met at the start of gene
# param metIn: Met in gene
# param stopEnd: stop codon at the end of gene
# param stopIn: stop codon in gene
# type num: integer
# type compStrandDNA: string
# type mRNA: string
# type protein: string
# type metStart: boolean
# type metIn: boolean
# type stopEnd: boolean
# type stopIn: boolean
read = ""
# beginning of reading frame
read += "Reading Frame #{}\n".format(num)
read += "RNA length: %i\n" % len(compStrandDNA)
# add color to mRNA
mRNAList = list(mRNA)
for letter in mRNAList:
letterIndex = mRNAList.index(letter)
if letter == "A":
mRNAList[letterIndex] = color('cyan') + letter + color('reset')
elif letter == "U":
mRNAList[letterIndex] = color('blue') + letter + color('reset')
elif letter == "C":
mRNAList[letterIndex] = color('bold red') + letter + color('reset')
elif letter == "G":
mRNAList[letterIndex] = color('bold magenta') + letter + color('reset')
mRNA = ''.join(mRNAList)
# continued beginning
read += "\tRNA:\t\t%s\n" % mRNA
lines = "| " * (len(compStrandDNA) // 3)
read += "\t\t\t\t %s\n" % lines
read += "\tProtein:\t%s\n\n" % protein
# summary for Met at start
if metStart == True:
read += "There is a Met at the start site.\n"
else:
read += "There is no Met at the start site.\n"
# summary for stop at end
if stopEnd == True:
read += "There is a stop at the end.\n"
else:
read += "There is no stop at the end.\n"
# summary for Met inside strand
if metIn == True:
read += "There is at least one Met somewhere other than at the start.\n"
else:
read += "There are no Mets other than at the start.\n"
# summary for stop inside strand
if stopIn == True:
read += "There is at least one stop interrupting the gene."
else:
read += "There are no interrupting stops."
return read
