def OnToggle(self, evt):
'''When any togglebutton is pressed'''
AA = []
clicked_color = '#A2CD5A'
unclicked_color = '#EEEEEE'
if self.Ala.GetValue():
AA.append('A')
self.Ala.SetBackgroundColour(clicked_color)
else:
self.Ala.SetBackgroundColour(unclicked_color)
if self.Val.GetValue():
AA.append('V')
self.Val.SetBackgroundColour(clicked_color)
else:
self.Val.SetBackgroundColour(unclicked_color)
if self.Ile.GetValue():
AA.append('I')
self.Ile.SetBackgroundColour(clicked_color)
else:
self.Ile.SetBackgroundColour(unclicked_color)
if self.Leu.GetValue():
AA.append('L')
self.Leu.SetBackgroundColour(clicked_color)
else:
self.Leu.SetBackgroundColour(unclicked_color)
if self.Met.GetValue():
AA.append('M')
self.Met.SetBackgroundColour(clicked_color)
else:
self.Met.SetBackgroundColour(unclicked_color)
if self.Phe.GetValue():
AA.append('F')
self.Phe.SetBackgroundColour(clicked_color)
else:
self.Phe.SetBackgroundColour(unclicked_color)
if self.Tyr.GetValue():
AA.append('Y')
self.Tyr.SetBackgroundColour(clicked_color)
else:
self.Tyr.SetBackgroundColour(unclicked_color)
if self.Trp.GetValue():
AA.append('W')
self.Trp.SetBackgroundColour(clicked_color)
else:
self.Trp.SetBackgroundColour(unclicked_color)
if self.Asp.GetValue():
AA.append('D')
self.Asp.SetBackgroundColour(clicked_color)
else:
self.Asp.SetBackgroundColour(unclicked_color)
if self.Glu.GetValue():
AA.append('E')
self.Glu.SetBackgroundColour(clicked_color)
else:
self.Glu.SetBackgroundColour(unclicked_color)
if self.Asn.GetValue():
AA.append('N')
self.Asn.SetBackgroundColour(clicked_color)
else:
self.Asn.SetBackgroundColour(unclicked_color)
if self.Gln.GetValue():
AA.append('Q')
self.Gln.SetBackgroundColour(clicked_color)
else:
self.Gln.SetBackgroundColour(unclicked_color)
if self.Ser.GetValue():
AA.append('S')
self.Ser.SetBackgroundColour(clicked_color)
else:
self.Ser.SetBackgroundColour(unclicked_color)
if self.Thr.GetValue():
AA.append('T')
self.Thr.SetBackgroundColour(clicked_color)
else:
self.Thr.SetBackgroundColour(unclicked_color)
if self.Arg.GetValue():
AA.append('R')
self.Arg.SetBackgroundColour(clicked_color)
else:
self.Arg.SetBackgroundColour(unclicked_color)
if self.His.GetValue():
AA.append('H')
self.His.SetBackgroundColour(clicked_color)
else:
self.His.SetBackgroundColour(unclicked_color)
if self.Lys.GetValue():
AA.append('K')
self.Lys.SetBackgroundColour(clicked_color)
else:
self.Lys.SetBackgroundColour(unclicked_color)
if self.Cys.GetValue():
AA.append('C')
self.Cys.SetBackgroundColour(clicked_color)
else:
self.Cys.SetBackgroundColour(unclicked_color)
if self.Gly.GetValue():
AA.append('G')
self.Gly.SetBackgroundColour(clicked_color)
else:
self.Gly.SetBackgroundColour(unclicked_color)
if self.Pro.GetValue():
AA.append('P')
self.Pro.SetBackgroundColour(clicked_color)
else:
self.Pro.SetBackgroundColour(unclicked_color)
if len(AA) > 0:
codon, target, offtarget, possibleAA = mbc.run(AA)
self.mixed_base_codon.SetReadOnly(False)
self.mixed_base_codon.SetText(codon)
self.mixed_base_codon.SetReadOnly(True)
targetstring = ''
for entry in target: #make string with the target AA
if targetstring == '':
targetstring += entry
else:
targetstring += ', ' + entry
offtargetstring = ''
for entry in offtarget: #make string with the offtarget AA
if offtargetstring == '':
offtargetstring += entry
else:
offtargetstring += ', ' + entry
self.target_hits.SetLabel('Target amino acids: ' + targetstring)
self.offtarget_hits.SetLabel('Off-target amino acids: ' +
offtargetstring)
#set the yellow buttons to indicate which AA are possible without further off-target hits
possible_color = '#FFFF99'
if 'A' in possibleAA and self.Ala.GetValue() == False:
self.Ala.SetBackgroundColour(possible_color)
if 'V' in possibleAA and self.Val.GetValue() == False:
self.Val.SetBackgroundColour(possible_color)
if 'I' in possibleAA and self.Ile.GetValue() == False:
self.Ile.SetBackgroundColour(possible_color)
if 'L' in possibleAA and self.Leu.GetValue() == False:
self.Leu.SetBackgroundColour(possible_color)
if 'M' in possibleAA and self.Met.GetValue() == False:
self.Met.SetBackgroundColour(possible_color)
if 'F' in possibleAA and self.Phe.GetValue() == False:
self.Phe.SetBackgroundColour(possible_color)
if 'Y' in possibleAA and self.Tyr.GetValue() == False:
self.Tyr.SetBackgroundColour(possible_color)
if 'W' in possibleAA and self.Trp.GetValue() == False:
self.Trp.SetBackgroundColour(possible_color)
if 'D' in possibleAA and self.Asp.GetValue() == False:
self.Asp.SetBackgroundColour(possible_color)
if 'E' in possibleAA and self.Glu.GetValue() == False:
self.Glu.SetBackgroundColour(possible_color)
if 'N' in possibleAA and self.Asn.GetValue() == False:
self.Asn.SetBackgroundColour(possible_color)
if 'Q' in possibleAA and self.Gln.GetValue() == False:
self.Gln.SetBackgroundColour(possible_color)
if 'S' in possibleAA and self.Ser.GetValue() == False:
self.Ser.SetBackgroundColour(possible_color)
if 'T' in possibleAA and self.Thr.GetValue() == False:
self.Thr.SetBackgroundColour(possible_color)
if 'R' in possibleAA and self.Arg.GetValue() == False:
self.Arg.SetBackgroundColour(possible_color)
if 'H' in possibleAA and self.His.GetValue() == False:
self.His.SetBackgroundColour(possible_color)
if 'K' in possibleAA and self.Lys.GetValue() == False:
self.Lys.SetBackgroundColour(possible_color)
if 'C' in possibleAA and self.Cys.GetValue() == False:
self.Cys.SetBackgroundColour(possible_color)
if 'G' in possibleAA and self.Gly.GetValue() == False:
self.Gly.SetBackgroundColour(possible_color)
if 'P' in possibleAA and self.Pro.GetValue() == False:
self.Pro.SetBackgroundColour(possible_color)
#make list of all codons in degenerate triplet
codonlist = dna.UnAmb(codon)
#count how many times each AA is coded for by these codons
self.AA_count = mbc.count_codon_list(codonlist)
#plot graph
self.update_plot()
else:
self.mixed_base_codon.SetReadOnly(False)
self.mixed_base_codon.SetText('None')
self.mixed_base_codon.SetReadOnly(True)
self.target_hits.SetLabel('Target amino acids: ')
self.offtarget_hits.SetLabel('Off-target amino acids: ')
self.AA_count = {
'A': 0,
'C': 0,
'E': 0,
'D': 0,
'G': 0,
'F': 0,
'I': 0,
'H': 0,
'K': 0,
'M': 0,
'L': 0,
'N': 0,
'Q': 0,
'P': 0,
'S': 0,
'R': 0,
'T': 0,
'W': 0,
'V': 0,
'Y': 0,
'stop': 0
}
self.update_plot()
def OnToggle(self, evt):
'''When any togglebutton is pressed'''
AA = []
clicked_color = '#A2CD5A'
unclicked_color = '#EEEEEE'
if self.Ala.GetValue():
AA.append('A')
self.Ala.SetBackgroundColour(clicked_color)
else:
self.Ala.SetBackgroundColour(unclicked_color)
if self.Val.GetValue():
AA.append('V')
self.Val.SetBackgroundColour(clicked_color)
else:
self.Val.SetBackgroundColour(unclicked_color)
if self.Ile.GetValue():
AA.append('I')
self.Ile.SetBackgroundColour(clicked_color)
else:
self.Ile.SetBackgroundColour(unclicked_color)
if self.Leu.GetValue():
AA.append('L')
self.Leu.SetBackgroundColour(clicked_color)
else:
self.Leu.SetBackgroundColour(unclicked_color)
if self.Met.GetValue():
AA.append('M')
self.Met.SetBackgroundColour(clicked_color)
else:
self.Met.SetBackgroundColour(unclicked_color)
if self.Phe.GetValue():
AA.append('F')
self.Phe.SetBackgroundColour(clicked_color)
else:
self.Phe.SetBackgroundColour(unclicked_color)
if self.Tyr.GetValue():
AA.append('Y')
self.Tyr.SetBackgroundColour(clicked_color)
else:
self.Tyr.SetBackgroundColour(unclicked_color)
if self.Trp.GetValue():
AA.append('W')
self.Trp.SetBackgroundColour(clicked_color)
else:
self.Trp.SetBackgroundColour(unclicked_color)
if self.Asp.GetValue():
AA.append('D')
self.Asp.SetBackgroundColour(clicked_color)
else:
self.Asp.SetBackgroundColour(unclicked_color)
if self.Glu.GetValue():
AA.append('E')
self.Glu.SetBackgroundColour(clicked_color)
else:
self.Glu.SetBackgroundColour(unclicked_color)
if self.Asn.GetValue():
AA.append('N')
self.Asn.SetBackgroundColour(clicked_color)
else:
self.Asn.SetBackgroundColour(unclicked_color)
if self.Gln.GetValue():
AA.append('Q')
self.Gln.SetBackgroundColour(clicked_color)
else:
self.Gln.SetBackgroundColour(unclicked_color)
if self.Ser.GetValue():
AA.append('S')
self.Ser.SetBackgroundColour(clicked_color)
else:
self.Ser.SetBackgroundColour(unclicked_color)
if self.Thr.GetValue():
AA.append('T')
self.Thr.SetBackgroundColour(clicked_color)
else:
self.Thr.SetBackgroundColour(unclicked_color)
if self.Arg.GetValue():
AA.append('R')
self.Arg.SetBackgroundColour(clicked_color)
else:
self.Arg.SetBackgroundColour(unclicked_color)
if self.His.GetValue():
AA.append('H')
self.His.SetBackgroundColour(clicked_color)
else:
self.His.SetBackgroundColour(unclicked_color)
if self.Lys.GetValue():
AA.append('K')
self.Lys.SetBackgroundColour(clicked_color)
else:
self.Lys.SetBackgroundColour(unclicked_color)
if self.Cys.GetValue():
AA.append('C')
self.Cys.SetBackgroundColour(clicked_color)
else:
self.Cys.SetBackgroundColour(unclicked_color)
if self.Gly.GetValue():
AA.append('G')
self.Gly.SetBackgroundColour(clicked_color)
else:
self.Gly.SetBackgroundColour(unclicked_color)
if self.Pro.GetValue():
AA.append('P')
self.Pro.SetBackgroundColour(clicked_color)
else:
self.Pro.SetBackgroundColour(unclicked_color)
if len(AA) > 0:
codon, target, offtarget, possibleAA = mbc.run(AA)
self.mixed_base_codon.SetReadOnly(False)
self.mixed_base_codon.SetText(codon)
self.mixed_base_codon.SetReadOnly(True)
targetstring = ''
for entry in target: #make string with the target AA
if targetstring == '':
targetstring += entry
else:
targetstring += ', '+entry
offtargetstring = ''
for entry in offtarget: #make string with the offtarget AA
if offtargetstring == '':
offtargetstring += entry
else:
offtargetstring += ', '+entry
self.target_hits.SetLabel('Target amino acids: '+targetstring)
self.offtarget_hits.SetLabel('Off-target amino acids: '+offtargetstring)
#set the yellow buttons to indicate which AA are possible without further off-target hits
possible_color = '#FFFF99'
if 'A' in possibleAA and self.Ala.GetValue() == False:
self.Ala.SetBackgroundColour(possible_color)
if 'V' in possibleAA and self.Val.GetValue() == False:
self.Val.SetBackgroundColour(possible_color)
if 'I' in possibleAA and self.Ile.GetValue() == False:
self.Ile.SetBackgroundColour(possible_color)
if 'L' in possibleAA and self.Leu.GetValue() == False:
self.Leu.SetBackgroundColour(possible_color)
if 'M' in possibleAA and self.Met.GetValue() == False:
self.Met.SetBackgroundColour(possible_color)
if 'F' in possibleAA and self.Phe.GetValue() == False:
self.Phe.SetBackgroundColour(possible_color)
if 'Y' in possibleAA and self.Tyr.GetValue() == False:
self.Tyr.SetBackgroundColour(possible_color)
if 'W' in possibleAA and self.Trp.GetValue() == False:
self.Trp.SetBackgroundColour(possible_color)
if 'D' in possibleAA and self.Asp.GetValue() == False:
self.Asp.SetBackgroundColour(possible_color)
if 'E' in possibleAA and self.Glu.GetValue() == False:
self.Glu.SetBackgroundColour(possible_color)
if 'N' in possibleAA and self.Asn.GetValue() == False:
self.Asn.SetBackgroundColour(possible_color)
if 'Q' in possibleAA and self.Gln.GetValue() == False:
self.Gln.SetBackgroundColour(possible_color)
if 'S' in possibleAA and self.Ser.GetValue() == False:
self.Ser.SetBackgroundColour(possible_color)
if 'T' in possibleAA and self.Thr.GetValue() == False:
self.Thr.SetBackgroundColour(possible_color)
if 'R' in possibleAA and self.Arg.GetValue() == False:
self.Arg.SetBackgroundColour(possible_color)
if 'H' in possibleAA and self.His.GetValue() == False:
self.His.SetBackgroundColour(possible_color)
if 'K' in possibleAA and self.Lys.GetValue() == False:
self.Lys.SetBackgroundColour(possible_color)
if 'C' in possibleAA and self.Cys.GetValue() == False:
self.Cys.SetBackgroundColour(possible_color)
if 'G' in possibleAA and self.Gly.GetValue() == False:
self.Gly.SetBackgroundColour(possible_color)
if 'P' in possibleAA and self.Pro.GetValue() == False:
self.Pro.SetBackgroundColour(possible_color)
#make list of all codons in degenerate triplet
codonlist = dna.UnAmb(codon)
#count how many times each AA is coded for by these codons
self.AA_count = mbc.count_codon_list(codonlist)
#plot graph
self.update_plot()
else:
self.mixed_base_codon.SetReadOnly(False)
self.mixed_base_codon.SetText('None')
self.mixed_base_codon.SetReadOnly(True)
self.target_hits.SetLabel('Target amino acids: ')
self.offtarget_hits.SetLabel('Off-target amino acids: ')
self.AA_count = {'A':0, 'C':0, 'E':0, 'D':0, 'G':0, 'F':0, 'I':0, 'H':0, 'K':0, 'M':0, 'L':0, 'N':0, 'Q':0, 'P':0, 'S':0, 'R':0, 'T':0, 'W':0, 'V':0, 'Y':0, 'stop':0}
self.update_plot()
def Draw(self, dc):
self.xc = self.size[0]/3 #centre of codon circle in x
self.yc = self.size[1]/2 #centre of codon circle in y
self.Radius = self.yc/1.2
target_color = '#CCFF66'
possible_color = '#FFFF66'
offtarget_color = '#FF9966'
nucleotide_color = '#8B835F'
coding_nucleotide_color = '#4B4424' #for coloring the nucleotides encoded by the ambigous codon
line_color = '#8B835F' #for lines
first_nucleotide_thickness = self.Radius/3
second_nucleotide_thickness = 2*(self.Radius/3)/3
third_nucleotide_thickness = 1*(self.Radius/3)/3
amino_acid_thickness = self.Radius/2.25
dc.SetBackground(wx.Brush("White"))
dc.Clear() # make sure you clear the bitmap!
gcdc = wx.GCDC(dc)
gcdc.SetPen(wx.Pen(colour='#666666', width=0))
#make a hidden dc to which features can be drawn in uinique colors and later used for hittests
self.hidden_dc = wx.MemoryDC()
self.hidden_dc.SelectObject(wx.EmptyBitmap(self.ClientSize[0], self.ClientSize[1]))
self.hidden_dc.SetBackground(wx.Brush("White"))
self.hidden_dc.Clear() # make sure you clear the bitmap!
#set up a dictionary to keep track of which color belongs to what object
self.catalog = {} #for matching features with the unique colors
self.catalog['(255, 255, 255, 255)'] = False #the background is white, have to add that key
unique_color = (0,0,0)
#draw reset button
## draw a reset button here ##
#draw first nucleotide
radius = first_nucleotide_thickness
thickness = first_nucleotide_thickness
font = wx.Font(pointSize=thickness/1.5, family=wx.FONTFAMILY_SWISS, style=wx.FONTWEIGHT_BOLD, weight=wx.FONTWEIGHT_BOLD)
gcdc.SetFont(font)
gcdc.SetBrush(wx.Brush("#ffe7ab"))
nucleotides = ['U', 'C', 'A', 'G']
for i in range(len(nucleotides)):
start_angle = 0 + 90*i
finish_angle = 90+90*i
pointlist = self.make_arc(self.xc, self.yc, start_angle, finish_angle, radius, thickness, step=5)
gcdc.DrawPolygon(pointlist)
x1, y1 = self.AngleToPoints(self.xc, self.yc, radius/2, finish_angle-(finish_angle-start_angle)/2)
#if nucleotide is part of degenerate codon it should have a different color
gcdc.SetTextForeground((nucleotide_color))
if self.codon is not False:
if nucleotides[i].replace('U','T') in dna.UnAmb(self.codon[0]):
gcdc.SetTextForeground((coding_nucleotide_color))
gcdc.DrawText(nucleotides[i], x1-radius/4, y1-radius/2.8)
#draw second nucleotide
radius = first_nucleotide_thickness+second_nucleotide_thickness
thickness = second_nucleotide_thickness
font = wx.Font(pointSize=thickness/2, family=wx.FONTFAMILY_SWISS, style=wx.FONTWEIGHT_BOLD, weight=wx.FONTWEIGHT_BOLD)
gcdc.SetFont(font)
gcdc.SetBrush(wx.Brush("#ffd976"))
nucleotides = ['UU', 'UC', 'UA', 'UG','CU', 'CC', 'CA', 'CG','AU', 'AC', 'AA', 'AG', 'GU', 'GC', 'GA', 'GG']
for i in range(len(nucleotides)):
start_angle = 0 + 22.5*i
finish_angle = 22.5+22.5*i
pointlist = self.make_arc(self.xc, self.yc, start_angle, finish_angle, radius, thickness, step=0.5)
gcdc.DrawPolygon(pointlist)
x1, y1 = self.AngleToPoints(self.xc, self.yc, radius/1.2, finish_angle-(finish_angle-start_angle)/2)
#if nucleotide is part of degenerate codon it should have a different color
gcdc.SetTextForeground((nucleotide_color))
if self.codon is not False:
# print('first')
# print('nuc', nucleotides[i].replace('U','T'))
# print('cod', dna.UnAmb(self.codon[0:2]))
if nucleotides[i].replace('U','T') in dna.UnAmb(self.codon[0:2]):
gcdc.SetTextForeground((coding_nucleotide_color))
gcdc.DrawText(nucleotides[i][1], x1-radius/14, y1-radius/10)
#draw third nucleotide
radius = first_nucleotide_thickness+second_nucleotide_thickness+third_nucleotide_thickness
thickness = third_nucleotide_thickness
font = wx.Font(pointSize=thickness/2, family=wx.FONTFAMILY_SWISS, style=wx.FONTWEIGHT_BOLD, weight=wx.FONTWEIGHT_BOLD)
gcdc.SetFont(font)
gcdc.SetBrush(wx.Brush("#ffc700"))
nucleotides = ['UUU', 'UUC', 'UUA', 'UUG','UCU', 'UCC', 'UCA', 'UCG','UAU', 'UAC', 'UAA', 'UAG', 'UGU', 'UGC', 'UGA', 'UGG',\
'CUU', 'CUC', 'CUA', 'CUG','CCU', 'CCC', 'CCA', 'CCG','CAU', 'CAC', 'CAA', 'CAG', 'CGU', 'CGC', 'CGA', 'CGG',\
'AUU', 'AUC', 'AUA', 'AUG','ACU', 'ACC', 'ACA', 'ACG','AAU', 'AAC', 'AAA', 'AAG', 'AGU', 'AGC', 'AGA', 'AGG',\
'GUU', 'GUC', 'GUA', 'GUG','GCU', 'GCC', 'GCA', 'GCG','GAU', 'GAC', 'GAA', 'GAG', 'GGU', 'GGC', 'GGA', 'GGG']
for i in range(len(nucleotides)):
start_angle = 0 + 5.625*i
finish_angle = 5.625+5.625*i
pointlist = self.make_arc(self.xc, self.yc, start_angle, finish_angle, radius, thickness, step=0.1)
gcdc.DrawPolygon(pointlist)
x1, y1 = self.AngleToPoints(self.xc, self.yc, radius/1.1, finish_angle-(finish_angle-start_angle)/2)
#if nucleotide is part of degenerate codon it should have a different color
gcdc.SetTextForeground((nucleotide_color))
if self.codon is not False:
if nucleotides[i].replace('U','T') in dna.UnAmb(self.codon):
gcdc.SetTextForeground((coding_nucleotide_color))
gcdc.DrawText(nucleotides[i][2], x1-radius/30, y1-radius/24)
#draw amino acids
radius = first_nucleotide_thickness+second_nucleotide_thickness+third_nucleotide_thickness+amino_acid_thickness
thickness = amino_acid_thickness
font = wx.Font(pointSize=third_nucleotide_thickness/2, family=wx.FONTFAMILY_SWISS, style=wx.FONTWEIGHT_NORMAL, weight=wx.FONTWEIGHT_NORMAL)
gcdc.SetFont(font)
gcdc.SetTextForeground(('#000000'))
AA = ['F', 'L', 'S', 'Y', 'stop', 'C', 'stop2', 'W', 'L2', 'P', 'H', 'Q', 'R', 'I', 'M', 'T', 'N', 'K', 'S2', 'R2', 'V', 'A', 'D', 'E', 'G']
AA_width = {'F':2, 'L':2, 'S':4, 'Y':2, 'stop':2, 'C':2, 'stop2':1, 'W':1, 'L2':4, 'P':4, 'H':2, 'Q':2, 'R':4, 'I':3, 'M':1, 'T':4, 'N':2, 'K':2, 'S2':2, 'R2':2, 'V':4, 'A':4, 'D':2, 'E':2, 'G':4}
AA_full = {'F':'Phenylalanine', 'L':'Leucine', 'S':'Serine', 'Y':'Tyrosine', 'stop':'Stop', 'C':'Cysteine', 'stop2':'Stop', 'W':'Tryptophan', 'L2':'Leucine', 'P':'Proline', 'H':'Histidine', 'Q':'Glutamine', 'R':'Arginine', 'I':'Isoleucine', 'M':'Methionine', 'T':'Threonine', 'N':'Asparagine', 'K':'Lysine', 'S2':'Serine', 'R2':'Arginine', 'V':'Valine', 'A':'Alanine', 'D':'Aspartic acid', 'E':'Glutamic acid', 'G':'Glycine'}
finish_angle = 0
#basic draw of the amino acid segments and names
for i in range(len(AA)):
#draw the amino acid segments
gcdc.SetPen(wx.Pen(colour='#666666', width=0))
if AA[i].replace('2','') in self.target: #if current AA is a selected one
gcdc.SetBrush(wx.Brush(target_color))
elif AA[i].replace('2','') in self.offtarget: #if it is in the off-targets list
gcdc.SetBrush(wx.Brush(offtarget_color))
elif AA[i].replace('2','') in self.possible: #if current AA is among the ones that may be selected without further off-targets
gcdc.SetBrush(wx.Brush(possible_color))
else: #otherwise use standard color
gcdc.SetBrush(wx.Brush("#fff2d1"))
start_angle = finish_angle
finish_angle = start_angle+5.625*AA_width[AA[i]]
pointlist = self.make_arc(self.xc, self.yc, start_angle, finish_angle, radius, thickness, step=0.1)
gcdc.DrawPolygon(pointlist)
#draw hidden color which is used for hittests
unique_color = self.GetNextRGB(unique_color) #get color for drawing unique colors on the hidden dc
self.catalog[str(unique_color+(255,))] = AA[i]
self.hidden_dc.SetPen(wx.Pen(colour=unique_color, width=0))
self.hidden_dc.SetBrush(wx.Brush(colour=unique_color))
self.hidden_dc.DrawPolygon(pointlist)
#draw lines
angle = start_angle
gcdc.SetPen(wx.Pen(colour=line_color, width=1))
if angle in [0,90,180,270]:
radius = 0
elif angle % 22.5 == 0:
radius = first_nucleotide_thickness
elif angle % 5.625 ==0:
radius = first_nucleotide_thickness+second_nucleotide_thickness
x1, y1 = self.AngleToPoints(self.xc, self.yc, radius, angle)
radius = radius = first_nucleotide_thickness+second_nucleotide_thickness+third_nucleotide_thickness+amino_acid_thickness
x2, y2 = self.AngleToPoints(self.xc, self.yc, radius, angle)
gcdc.DrawLine(x1, y1, x2, y2)
#draw text
text_angle = finish_angle-(finish_angle-start_angle)/2
if finish_angle <= 180:
text_extent = gcdc.GetTextExtent(AA_full[AA[i]])
text_radius = (first_nucleotide_thickness+second_nucleotide_thickness+third_nucleotide_thickness)*1.05
#need to adjust for text height. Imagine right angled triangle. Adjecent is radius. Opposite is half of the text height. Calculate tan angle.
tanangle = (0.5*text_extent[1])/text_radius #calculate the Tan(angle)
radians = math.atan(tanangle) #negate the Tin part and get radians
degrees = radians*(180/math.pi) #convert radians to degrees
text_position_angle = text_angle-degrees
tx, ty = self.AngleToPoints(self.xc, self.yc, text_radius, text_position_angle)
gcdc.DrawRotatedText(AA_full[AA[i]], tx, ty, -text_angle+90)
else:
text_extent = gcdc.GetTextExtent(AA_full[AA[i]])
text_radius = (first_nucleotide_thickness+second_nucleotide_thickness+third_nucleotide_thickness)*1.05 + text_extent[0]
#need to adjust for text height. Imagine right angled triangle. Adjecent is radius. Opposite is half of the text height. Calculate tan angle.
tanangle = (0.5*text_extent[1])/text_radius #calculate the Tan(angle)
radians = math.atan(tanangle) #negate the Tin part and get radians
degrees = radians*(180/math.pi) #convert radians to degrees
text_position_angle = text_angle+degrees
tx, ty = self.AngleToPoints(self.xc, self.yc, text_radius, text_position_angle)
gcdc.DrawRotatedText(AA_full[AA[i]], tx, ty, -text_angle-90)
#now draw the highlighted ones
finish_angle = 0
gcdc.SetPen(wx.Pen(colour='#FF0000', width=1))
gcdc.SetBrush(wx.Brush(colour=(0,0,0,0)))
for i in range(len(AA)):
#if current AA is highlighted, redraw that segment with a different pen
start_angle = finish_angle
finish_angle = start_angle+5.625*AA_width[AA[i]]
if AA[i].replace('2', '') == self.highlighted: #if highlighted AA is the current one
pointlist = self.make_arc(self.xc, self.yc, start_angle, finish_angle, radius, thickness, step=0.1)
gcdc.DrawPolygon(pointlist)
#write what the ambigous codon is
point_size = int(self.Radius/8)
font = wx.Font(pointSize=point_size, family=wx.FONTFAMILY_SWISS, style=wx.ITALIC, weight=wx.FONTWEIGHT_NORMAL)
gcdc.SetFont(font)
gcdc.SetTextForeground((line_color))
x = self.size[0]*0.62
y = self.size[1]*0.1
text = 'Codon:'
gcdc.DrawText(text, x, y)
x = self.size[0]*0.75
point_size = int(self.Radius/6)
font = wx.Font(pointSize=point_size, family=wx.FONTFAMILY_SWISS, style=wx.FONTWEIGHT_BOLD, weight=wx.FONTWEIGHT_BOLD)
gcdc.SetFont(font)
gcdc.SetTextForeground((coding_nucleotide_color))
if self.codon is False:
text = ''
else:
text = self.codon
gcdc.DrawText(text, x, y)
#and the bases they code for
if self.codon is not False:
#get text position based on the ambigous codon
first_x = x + gcdc.GetTextExtent(text[0:1])[0] - gcdc.GetTextExtent(text[0])[0]/2
second_x = x + gcdc.GetTextExtent(text[0:2])[0] - gcdc.GetTextExtent(text[1])[0]/2
third_x = x + gcdc.GetTextExtent(text[0:3])[0] - gcdc.GetTextExtent(text[2])[0]/2
start_y = y + gcdc.GetTextExtent(text[0])[1]
#set new text size
point_size = int(self.Radius/18)
font = wx.Font(pointSize=point_size, family=wx.FONTFAMILY_SWISS, style=wx.FONTSTYLE_ITALIC, weight=wx.FONTWEIGHT_NORMAL)
gcdc.SetFont(font)
gcdc.SetTextForeground((coding_nucleotide_color))
first = dna.UnAmb(self.codon[0])
second = dna.UnAmb(self.codon[1])
third = dna.UnAmb(self.codon[2])
first_y = start_y
for i in range(0, len(first)):
text = first[i]
#adjust for the size of that text
pos_x = first_x - gcdc.GetTextExtent(text)[0]/2
gcdc.DrawText(text, pos_x, first_y)
first_y += point_size
second_y = start_y
for i in range(0, len(second)):
text = second[i]
#adjust for the size of that text
pos_x = second_x - gcdc.GetTextExtent(text)[0]/2
gcdc.DrawText(text, pos_x, second_y)
second_y += point_size
third_y = start_y
for i in range(0, len(third)):
text = third[i]
#adjust for the size of that text
pos_x = third_x - gcdc.GetTextExtent(text)[0]/2
gcdc.DrawText(text, pos_x, third_y)
third_y += point_size
#draw key
width = self.Radius/16
height = self.Radius/16
point_size = int(self.Radius/20)
font = wx.Font(pointSize=point_size, family=wx.FONTFAMILY_SWISS, style=wx.FONTWEIGHT_NORMAL, weight=wx.FONTWEIGHT_NORMAL)
gcdc.SetFont(font)
gcdc.SetTextForeground(('#666666'))
#target key
text = 'Target AA'
x = 10
y = 10
gcdc.SetBrush(wx.Brush(target_color))
gcdc.SetPen(wx.Pen(colour='#666666', width=0))
gcdc.DrawRectangle(x, y, width, height)
gcdc.DrawText(text, x+width*1.2, y)
#possible key
text = 'Possible AA'
x = 10
y += point_size*1.5
gcdc.SetBrush(wx.Brush(possible_color))
gcdc.SetPen(wx.Pen(colour='#E6E65C', width=1))
gcdc.DrawRectangle(x, y, width, height)
gcdc.DrawText(text, x+width*1.2, y)
#possible key
text = 'Off-target AA'
x = 10
y += point_size*1.5
gcdc.SetBrush(wx.Brush(offtarget_color))
gcdc.SetPen(wx.Pen(colour='#666666', width=0))
gcdc.DrawRectangle(x, y, width, height)
gcdc.DrawText(text, x+width*1.2, y)
## draw graph ##
AA_order = ('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y', 'stop')
AA_full = {'F':'Phenylalanine', 'L':'Leucine', 'S':'Serine', 'Y':'Tyrosine', 'stop':'Stop', 'C':'Cysteine', 'stop2':'Stop', 'W':'Tryptophan', 'L2':'Leucine', 'P':'Proline', 'H':'Histidine', 'Q':'Glutamine', 'R':'Arginine', 'I':'Isoleucine', 'M':'Methionine', 'T':'Threonine', 'N':'Asparagine', 'K':'Lysine', 'S2':'Serine', 'R2':'Arginine', 'V':'Valine', 'A':'Alanine', 'D':'Aspartic acid', 'E':'Glutamic acid', 'G':'Glycine'}
originx = self.size[0]*0.75 #centre of plot in x
originy = self.size[1]*0.45 #centre of plot in y
sizex = self.size[0]*0.2
sizey = self.size[1]*0.5
xspacing = sizex/7
yspacing = float(sizey)/float(21)
tick_size = sizex/30
#draw background rectangle
gcdc.SetBrush(wx.Brush("#fff2d1"))
gcdc.SetPen(wx.Pen(colour=line_color, width=0))
gcdc.DrawRectangle(originx, originy, sizex, sizey)
#frame
gcdc.SetPen(wx.Pen(line_color))
gcdc.DrawLine(originx, originy, originx+sizex, originy) #top line... #DrawLine(self, x1, y1, x2, y2)
gcdc.DrawLine(originx+sizex, originy, originx+sizex, originy+sizey) #right line
gcdc.DrawLine(originx+sizex, originy+sizey, originx, originy+sizey) #bottom line
gcdc.DrawLine(originx, originy+sizey, originx, originy) #left line
#title
point_size = int(sizex/12)
font = wx.Font(pointSize=point_size, family=wx.FONTFAMILY_SWISS, style=wx.FONTWEIGHT_NORMAL, weight=wx.FONTWEIGHT_NORMAL)
gcdc.SetFont(font)
gcdc.SetTextForeground((line_color))
title = 'Codon count for each AA'
gcdc.DrawText(title, originx, originy-gcdc.GetTextExtent(text)[1]*2)
#y labels (amino acids)
point_size = int(self.Radius/18)
font = wx.Font(pointSize=point_size, family=wx.FONTFAMILY_SWISS, style=wx.FONTWEIGHT_NORMAL, weight=wx.FONTWEIGHT_NORMAL)
gcdc.SetFont(font)
gcdc.SetTextForeground((line_color))
for i in range(0, 21):
amino_acid = AA_full[str(AA_order[i])]
gcdc.DrawText(amino_acid, originx-gcdc.GetTextExtent(amino_acid)[0]-tick_size, originy+(yspacing*i)-gcdc.GetTextExtent(amino_acid)[1]/2+yspacing/2)
#x labels (count)
for i in range(1, 7):
gcdc.DrawText(str(i), originx+xspacing*i-gcdc.GetTextExtent('6')[0]/2, originy-gcdc.GetTextExtent('6')[1]-tick_size/2)
#x ticks
# for i in range(1, 7):
# gcdc.DrawLine(originx+(xspacing*i), originy, originx+(xspacing*i), originy+tick_size)
# gcdc.DrawLine(originx+(xspacing*i), originy+sizey, originx+(xspacing*i), originy+sizey-tick_size)
# #y ticks
# for i in range(1, 22):
# gcdc.DrawLine(originx, originy+(yspacing*i), originx+tick_size, originy+(yspacing*i))
# gcdc.DrawLine(originx+sizex, originy+(yspacing*i), originx+sizex-tick_size, originy+(yspacing*i))
#draw bars
if self.codon is not False:
self.AA_count = mbc.count_codon_list(dna.UnAmb(self.codon))
for i in range(0, 21):
AA = AA_order[i]
if AA in self.target: #if current AA is a selected one
gcdc.SetBrush(wx.Brush(target_color))
elif AA in self.offtarget: #if it is in the off-targets list
gcdc.SetBrush(wx.Brush(offtarget_color))
else:
gcdc.SetBrush(wx.Brush('#666666'))
count = self.AA_count[AA]
gcdc.DrawRectangle(originx, originy+yspacing*i+yspacing*0.1, count*xspacing, yspacing*0.8) #(x, y, w, h)
