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quwubin/CairoNumberWidth.py

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Virtual electrophotogram
Raw
CairoNumberWidth.py
#!/home/zhangcg/local/python/bin/python
# -*- coding:utf-8 -*-
#-----------------------------------------------------
# File: CairoNumberWidth.py
# Date: 2008-07-04
# Description:
#-----------------------------------------------------
__version__ = '1.0'
__author__ = 'Wubin Qu <[email protected]> @ZCGLAB @BMI @CHINA'
__blog__ = 'http://quwubin.cnblogs.com'
__license__ = 'GPL'
font50 = {
"a" : 23.0,
"b" : 26.0,
"c" : 22.0,
"d" : 25.0,
"e" : 22.0,
"f" : 17.0,
"g" : 24.0,
"h" : 26.0,
"i" : 14.0,
"j" : 14.0,
"k" : 25.0,
"l" : 14.0,
"m" : 39.0,
"n" : 25.0,
"o" : 24.0,
"p" : 25.0,
"q" : 25.0,
"r" : 17.0,
"s" : 20.0,
"t" : 15.0,
"u" : 25.0,
"v" : 25.0,
"w" : 36.0,
"x" : 25.0,
"y" : 25.0,
"z" : 22.0,
"0" : 25.0,
"1" : 26.0,
"2" : 25.0,
"3" : 25.0,
"4" : 25.0,
"5" : 25.0,
"6" : 25.0,
"7" : 25.0,
"8" : 26.0,
"9" : 25.0,
"A" : 36.0,
"B" : 34.0,
"C" : 33.0,
"D" : 36.0,
"E" : 30.0,
"F" : 28.0,
"G" : 36.0,
"H" : 35.0,
"I" : 16.0,
"J" : 19.0,
"K" : 36.0,
"L" : 30.0,
"M" : 44.0,
"N" : 36.0,
"O" : 37.0,
"P" : 28.0,
"Q" : 37.0,
"R" : 33.0,
"S" : 28.0,
"T" : 30.0,
"U" : 36.0,
"V" : 36.0,
"W" : 47.0,
"X" : 36.0,
"Y" : 36.0,
"Z" : 31.0,
"_" : 25.0,
"-" : 16.0,
"|" : 9.0,
"!" : 16.0,
"@" : 47.0,
"#" : 27.0,
"$" : 25.0,
"%" : 41.0,
"^" : 23.0,
"&" : 39.0,
"*" : 26.0,
"(" : 16.0,
")" : 17.0,
"+" : 28.0,
"[" : 17.0,
"]" : 16.0,
"{" : 24.0,
"}" : 24.0,
":" : 14.0,
'"' : 21.0,
";" : 14.0,
"'" : 9.0,
"\\" : 14.0,
"," : 13.0,
"." : 12.0,
"/" : 14.0,
"?" : 22.0,
">" : 28.0,
"<" : 28.0,
}
font30 = {
" " : 14.0,
"a" : 14.0,
"b" : 15.0,
"c" : 13.0,
"d" : 15.0,
"e" : 14.0,
"f" : 10.0,
"g" : 15.0,
"h" : 15.0,
"i" : 8.0,
"j" : 9.0,
"k" : 16.0,
"l" : 9.0,
"m" : 24.0,
"n" : 15.0,
"o" : 15.0,
"p" : 15.0,
"q" : 15.0,
"r" : 10.0,
"s" : 12.0,
"t" : 8.0,
"u" : 15.0,
"v" : 15.0,
"w" : 22.0,
"x" : 15.0,
"y" : 15.0,
"z" : 13.0,
"0" : 15.0,
"1" : 15.0,
"2" : 15.0,
"3" : 15.0,
"4" : 16.0,
"5" : 14.0,
"6" : 15.0,
"7" : 15.0,
"8" : 15.0,
"9" : 15.0,
"A" : 22.0,
"B" : 19.0,
"C" : 20.0,
"D" : 21.0,
"E" : 19.0,
"F" : 17.0,
"G" : 21.0,
"H" : 21.0,
"I" : 9.0,
"J" : 12.0,
"K" : 22.0,
"L" : 18.0,
"M" : 26.0,
"N" : 21.0,
"O" : 21.0,
"P" : 17.0,
"Q" : 21.0,
"R" : 20.0,
"S" : 17.0,
"T" : 19.0,
"U" : 21.0,
"V" : 22.0,
"W" : 28.0,
"X" : 22.0,
"Y" : 21.0,
"Z" : 19.0,
"_" : 15.0,
"-" : 9.0,
"|" : 6.0,
"!" : 10.0,
"@" : 27.0,
"#" : 17.0,
"$" : 15.0,
"%" : 25.0,
"^" : 14.0,
"&" : 23.0,
"*" : 15.0,
"(" : 10.0,
")" : 10.0,
"+" : 17.0,
"[" : 11.0,
"]" : 10.0,
"{" : 15.0,
"}" : 15.0,
":" : 8.0,
'"' : 12.0,
";" : 8.0,
"'" : 5.0,
"\\" : 8.0,
"," : 8.0,
"." : 7.0,
"/" : 8.0,
"?" : 14.0,
">" : 17.0,
"<" : 17.0,
}
font20 = {
" " : 9.0,
"a" : 9.0,
"b" : 10.0,
"c" : 9.0,
"d" : 11.0,
"e" : 9.0,
"f" : 7.0,
"g" : 11.0,
"h" : 9.0,
"i" : 6.0,
"j" : 6.0,
"k" : 10.0,
"l" : 6.0,
"m" : 16.0,
"n" : 11.0,
"o" : 10.0,
"p" : 11.0,
"q" : 10.0,
"r" : 7.0,
"s" : 8.0,
"t" : 5.0,
"u" : 10.0,
"v" : 10.0,
"w" : 14.0,
"x" : 10.0,
"y" : 10.0,
"z" : 9.0,
"0" : 11.0,
"1" : 10.0,
"2" : 10.0,
"3" : 10.0,
"4" : 11.0,
"5" : 10.0,
"6" : 10.0,
"7" : 10.0,
"8" : 10.0,
"9" : 11.0,
"A" : 14.0,
"B" : 12.0,
"C" : 14.0,
"D" : 15.0,
"E" : 12.0,
"F" : 12.0,
"G" : 15.0,
"H" : 14.0,
"I" : 6.0,
"J" : 8.0,
"K" : 14.0,
"L" : 12.0,
"M" : 17.0,
"N" : 14.0,
"O" : 14.0,
"P" : 11.0,
"Q" : 14.0,
"R" : 13.0,
"S" : 10.0,
"T" : 12.0,
"U" : 14.0,
"V" : 14.0,
"W" : 19.0,
"X" : 14.0,
"Y" : 14.0,
"Z" : 13.0,
"_" : 10.0,
"-" : 7.0,
"|" : 4.0,
"!" : 7.0,
"@" : 18.0,
"#" : 12.0,
"$" : 10.0,
"%" : 16.0,
"^" : 9.0,
"&" : 16.0,
"*" : 10.0,
"(" : 7.0,
")" : 7.0,
"+" : 12.0,
"[" : 7.0,
"]" : 7.0,
"{" : 10.0,
"}" : 10.0,
":" : 6.0,
'"' : 8.0,
";" : 6.0,
"'" : 4.0,
"\\" : 6.0,
"," : 5.0,
"." : 4.0,
"/" : 6.0,
"?" : 9.0,
">" : 12.0,
"<" : 12.0,
}
Raw
GelMobility.py
#!/home/zhangcg/local/python/bin/python
# -*- coding: utf-8 -*- #
'''Mobility of the PCR amplicons in agarose gel electrophoresis
was calculated following the semi-log formula reported by Helling
et al [Ref. 1] in 1974.
Y = a - b * ln (X + k)
Where Y is the mobility and X is the size of the PCR amplicons.
To get an reliable prediction of mobility of PCR amplicons, we
determined these parameters (a, b and k) by statistically analyzing
the commercially available DNA markers of known size (100 bp, 250 bp,
500 bp, 750 bp, 1000 bp and 2000 bp, from TaKaRa Inc.) in agarose gel
with different concentrations. The DNA fragment of 100 bp was taken as
a reference band in the agarose gel electrophoresis, and the relative
mobility was determined according to the 100 bp DNA band. When the
mobility of the reference band reached 5 cm in running the agarose gel,
the electrophoresis was stoped and the mobility of other DNA bands
were measure to determine the relative mobility. Briefly, the
parameters in the abovementioned formula were determined on the
0.5% ~ 2% agarose gel electrophoresis with triplicate measurements
in out lab and shown below for producing the virtual electrophoretogram
in MPprimer program.
For 0.5% agarose gel concentration:
a = 2.7094
b = 0.2691
k = 464.4412
R^2 = 0.9989
For 1.0% agarose gel concentration:
a = 2.3977
b = 0.2700
k = 73.9788
R^2 = 0.9984
For 1.5% agarose gel concentration:
a = 2.3221
b = 0.2634
k = 48.0873
R^2 = 0.9977
For 2.0% agarose gel concentration:
a = 2.1333
b = 0.2561
k = 18.5417
R^2 = 0.9948
Reference
[1] Helling, R. B., Goodman, H. M., & Boyer, H. W. (1974). Analysis of
endonuclease R-EcoRI fragments of DNA from lambdoid bacteriophages and
other viruses by agarose-gel electrophoresis. Journal of Virology,
14(5): 1235-1244.
'''
# Author: Wubin Qu [[email protected]], BIRM, China
# Date: 2009-10-12
# License: GPL v3
import sys
def load_gel_para_dict(gel_conc=1.0, formula='Helling'):
gel_para_dict = {}
gel_para_dict['Helling'] = {}
# Parameter for Helling's formula
gel_para = {}
gel_para[0.5] = {
'a' : 2.7094,
'b' : 0.2691,
'k' : 464.4412,
}
gel_para[1.0] = {
'a' : 2.3977,
'b' : 0.2700,
'k' : 73.9788,
}
gel_para[1.5] = {
'a' : 2.3221,
'b' : 0.2634,
'k' : 48.0873,
}
gel_para[2.0] = {
'a' : 2.1333,
'b' : 0.2561,
'k' : 18.5417,
}
gel_para_dict['Helling'] = gel_para
err_msg = 'Gel concentration or formula is illegal, Currently, only 0.5, 1, 1.5, 2.0 for concentration and "Helling" for formula are allowed.'
try:
gel_conc = float(gel_conc)
a = gel_para_dict[formula][gel_conc]['a']
b = gel_para_dict[formula][gel_conc]['b']
k = gel_para_dict[formula][gel_conc]['k']
except:
print >> sys.stderr, err_msg
exit()
return gel_para_dict, a, b, k
def get_size_range(size, gel_conc=1.0, ref_mobility=50, offset=2, formula='Helling'):
Y = cal_mobility(size, gel_conc)
offset = int(offset)
# Set 2 mm as the distance which the bands can be \
#seperated by naked eyes
Xmin = cal_size(Y + offset, gel_conc=gel_conc, ref_mobility=ref_mobility, formula='Helling')
Xmax = cal_size(Y - offset, gel_conc=gel_conc, ref_mobility=ref_mobility, formula='Helling')
return Xmin, Xmax
def cal_mobility(X, gel_conc=1.0, ref_mobility=50, formula='Helling'):
'''Cal mobility based on size'''
import math
gel_para_dict, a, b, k = load_gel_para_dict(gel_conc=gel_conc, formula=formula)
X = float(X)
gel_conc = float(gel_conc)
# X: size (bp)
# ref_mobility: the mobility distance of the fastest DNA segment
if formula == 'Helling':
Y = a - b * math.log(X + k)
else:
pass
#Y = math.exp(a - b * math.log(X + k))
# Y: the relative mobility = mobility distance / ref_mobility
Y = Y * ref_mobility
# Y: the mobility distance
return round(Y, 1)
def cal_size(Y, gel_conc=1.0, ref_mobility=50, formula='Helling'):
'''Predict size based on the relative mobility'''
import math
gel_para_dict, a, b, k = load_gel_para_dict(gel_conc=gel_conc, formula=formula)
# Y: the mobility distance
Y = Y / ref_mobility
# ref_mobility: the mobility distance of the fastest DNA segment
if formula == 'Helling':
#Y = a - b * math.log(X + k)
X = math.exp((a - Y) / b) - k
else:
pass
return int(round(X, 0))
def main ():
'''Test'''
import sys
#X = 100
#gel_conc = sys.argv[1]
#mobility = cal_mobility(X, gel_conc, ref_mobility=50, formula='Helling')
#print mobility
#mobility = cal_mobility(X, gel_conc, ref_mobility=50)
#print mobility
min, max = get_size_range(sys.argv[2], gel_conc=1.0, ref_mobility=50, offset=sys.argv[1], formula='Helling')
print min, max
if __name__ == '__main__':
main()
Raw
ve.py
#!/home/zhangcg/local/python/bin/python
# -*- coding:utf-8 -*-
from __future__ import division
__version__ = '1.0'
__author__ = 'Wubin Qu <[email protected]>'
__license__ = 'GPL v3'
import os
import time
import CairoNumberWidth as CNW
import cairo
import GelMobility
def draw_title(ctx, height, width):
'''Draw title'''
title = 'Virtual Electrophotogram'
title_length = 0
for i in range(len(title)):
title_length = title_length + CNW.font30[title[i]]
ctx.move_to(width/2 - title_length/2, 50)
ctx.set_source_rgb(0, 0, 237)
ctx.select_font_face("Times", cairo.FONT_SLANT_NORMAL)
ctx.set_font_size(30)
ctx.show_text(title)
ISOTIMEFORMAT = '%Y-%m-%d %X'
title = 'Created by VE @ %s' % time.strftime(ISOTIMEFORMAT, time.localtime(time.time()))
title_length = 0
for i in range(len(title)):
title_length = title_length + CNW.font20[title[i]]
ctx.move_to(width/2 - title_length/2, 80)
ctx.set_source_rgb(0, 0, 237)
ctx.select_font_face("Times", cairo.FONT_SLANT_NORMAL)
ctx.set_font_size(20)
ctx.show_text(title)
ctx.stroke()
return ctx
def draw_foot(ctx, height, width, agarose, product_number):
'''Draw title'''
title = 'M: Marker DL2000, %s agarose gel' % agarose
title_length = 0
for i in range(len(title)):
title_length = title_length + CNW.font20[title[i]]
ctx.move_to(width/2 - title_length/2, 715)
ctx.set_source_rgb(1, 1, 1)
ctx.select_font_face("Times", cairo.FONT_SLANT_NORMAL)
ctx.set_font_size(20)
ctx.show_text(title)
ctx.stroke()
title = '1-%s: PCR amplicons' % (product_number + 1)
title_length = 0
for i in range(len(title)):
title_length = title_length + CNW.font20[title[i]]
ctx.move_to(width/2 - title_length/2, 738)
ctx.set_source_rgb(1, 1, 1)
ctx.select_font_face("Times", cairo.FONT_SLANT_NORMAL)
ctx.set_font_size(20)
ctx.show_text(title)
ctx.stroke()
return ctx
def draw_virtual_elec(ctx, height, width, idname_size, agarose, product_number):
'''Draw'''
# Draw slot
ctx.select_font_face("Times", cairo.FONT_SLANT_NORMAL)
x = 30 + 80
y = 160
for i in range(product_number + 2):
ctx.set_source_rgba(0, 0, 0, 1.0)
ctx.rectangle(x, y, 70, 500)
ctx.fill()
x = x + 90
x = 30 + 80
y = 160
for i in range(product_number + 2):
if i == 0:
line_title = 'M'
else:
line_title = str(i)
line_title_length = 0
for j in range(len(line_title)):
line_title_length = line_title_length + CNW.font20[line_title[j]]
ctx.move_to(x + 35 - line_title_length/2, y-10)
ctx.set_source_rgb(1, 1, 1)
ctx.set_font_size(20)
ctx.show_text(line_title)
if i != 0 and i <= product_number:
id, size = idname_size[i-1]
y1 = GelMobility.cal_mobility(size, gel_conc=agarose, ref_mobility=50, formula='Helling')
y1 = y1*13 - 40# 13 is just a amplificationfactor
ctx.move_to(x+10, y1)
ctx.set_line_width(6)
ctx.line_to(x + 50, y1)
x2 = 30 + 80 + 90 * (product_number + 1) + 10
ctx.move_to(x2, y1)
ctx.set_line_width(6)
ctx.line_to(x2 + 50, y1)
ctx.stroke()
x3 = 30 + 80 + 90 * (product_number + 2)
ctx.move_to(x3, y1+4)
bp_num = str(size).rjust(4) + ' bp'
#bp_num = size + ' bp'
ctx.show_text(bp_num)
ctx.stroke()
y4 = y + 525
id_length = 0
for i in range(len(id)):
id_length = id_length + CNW.font20[id[i]]
ctx.move_to(x + 35 - id_length/2, y4)
ctx.set_source_rgb(1, 1, 1)
ctx.set_font_size(20)
ctx.show_text(id)
x = x + 90
# Mark 2000 kb
mark_size_list = [2000, 1000, 750, 500, 250, 100]
mark_size_dict = {
2000 : '2000 bp',
1000 : '1000 bp',
750 : ' 750 bp',
500 : ' 500 bp',
250 : ' 250 bp',
100 : ' 100 bp',
}
ctx.set_source_rgb(1, 1, 1)
for mark_size in mark_size_list:
x = 30 + 80 + 10
y = GelMobility.cal_mobility(mark_size, gel_conc=agarose, ref_mobility=50, formula='Helling')
y = y*13 - 40# 13 is just a amplificationfactor
ctx.move_to(x, y)
#x, y = ctx.get_current_point()
ctx.set_line_width(6)
ctx.line_to(x + 50, y)
ctx.stroke()
ctx.move_to(x - 90, y+4)
ctx.show_text(mark_size_dict[mark_size])
ctx.stroke()
return ctx
def paint(size_list, agarose, pic_path):
'''Paint the virtual electrophotogram '''
size_list = list(set(size_list))
size_list.sort()
idname_size = [(str(size), size) for size in size_list]
height = 750
# Marker line width: 80
product_number = len(idname_size)
width = (product_number + 2) * 90 + 80 + 60 + 80
# Set cairo
surface = cairo.ImageSurface(cairo.FORMAT_ARGB32, width, height)
ctx = cairo.Context(surface)
# Mask
ctx.set_source_rgba(0, 0, 0, 0.9)
ctx.rectangle(0, 100, width, height)
ctx.fill()
ctx = draw_title(ctx, height, width)
ctx = draw_virtual_elec(ctx, height, width, idname_size, agarose, product_number)
ctx = draw_foot(ctx, height, width, agarose, product_number)
#output a PNG file
surface.write_to_png(pic_path)
return pic_path
def main ():
size_list = [100, 200, 300, 400, 500]
agarose = 1
pic_path = 've.png'
ele_picture = paint(size_list, agarose, pic_path)
if __name__ == '__main__':
main()
@quwubin
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Author

quwubin commented Mar 21, 2014

Download these three script and put them into a directory.

Run ./ve.py to get an example virtual electrophotogram called "ve.png".

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