scripts/experimental_gel2.py
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2013 by Björn Johansson. All rights reserved.
# This code is part of the Python-dna distribution and governed by its
# license. Please see the LICENSE.txt file that should have been included
# as part of this package.
"""
This module contain experimental functionality for smulation of agarose gel electrophoresis of DNA.
Note
----
This code is in a very early stage of development and documentation.
Read the source code to get an idea for how it works.
"""
try:
import pygame
except ImportError:
pass
import math
import webbrowser
def gamma(x, t, k=1):
b = 1.0 / t
x = x * k
c = 0.0
for i in range(0, k):
c += (math.exp(-b * x) * (b * x) ** i) / math.factorial(i)
return c
def testColour(c):
"""Convert integer to colour, which saturates if > 255"""
if c <= 255:
return (c, c, c)
else:
return (255, 255, 255)
# def display(width, height, image):
# """ Create a Pygame image of dimensions width x height and show image """
#
# screen = pygame.display.set_mode((width, height))
# screen.blit(image, (60, 30))
# pygame.display.flip()
# running = True
# while running:
# for event in pygame.event.get():
# if event.type == pygame.QUIT:
# running = False
class Gel:
"""A Gel contains lanes into which DNA can be loaded and run.
The Gel is exposured to see the location and intensity of DNA."""
LANE_WIDTH = 30.0
LANE_HEIGHT = 6
LANE_MARGIN = 6
BORDER = 40
def __init__(self, size, agarose=1):
self.y = size[0]
self.x = 2 * Gel.BORDER + size[1] * (Gel.LANE_WIDTH + Gel.LANE_MARGIN) - Gel.LANE_MARGIN
self.agarose = agarose # Should test whether value is reasonable (say, 0.5% - 3%)
self.optimum_DNA_length = 2000 / agarose**3 # Best separate based on agarose hole size
self.samples = []
self.lanes = []
for n in range(size[1]):
self.samples.append([])
self.lanes.append([])
for lane in self.lanes:
for n in range(Gel.BORDER, self.y + 3):
lane.append(0.0)
def loadSample(self, lane, sample):
"""Add list containing tuple of DNA length and concentrations to lane in gel."""
for dna in sample:
strand = {
"length": float(dna[0]),
"conc": dna[1] * 1.0 / Gel.LANE_HEIGHT,
"position": Gel.BORDER + 1,
}
self.samples[lane - 1].append(strand)
def run(self, time=30.0, voltage=20.0):
"""Move loaded DNA down the gel at a rate dependent on voltage, DNA length and agarose concentration."""
max_dist = 0.25 * time * voltage
for sample in self.samples:
for dna in sample:
g = gamma(dna["length"] / 20, int(self.optimum_DNA_length / 20))
dna["position"] += max_dist * g
def expose(self, exposure=0.1, aperture=2):
"""Returns an image of the gel with the DNA highlighted"""
c1, c2 = exposure * 100, exposure * 200
fill_colour = (c1, c1, c2)
image = pygame.Surface((self.x + 2, self.y + 2))
pygame.draw.rect(image, fill_colour, (1, 1, self.x, self.y), 0)
edge_colour = (140, 140, 150)
edges = pygame.Surface((self.x + 2, self.y + 2))
edges.set_colorkey((0, 0, 0))
edges.set_alpha(120)
pygame.draw.rect(image, edge_colour, (0, 0, self.x + 2, self.y + 2), 1)
self._findDNAConcentrations(c1)
x = Gel.BORDER + 1
for lane in self.lanes:
for position in range(len(lane)):
if lane[position] > 0:
brightness = lane[position] * exposure / aperture + c1
colour1 = testColour(brightness)
colour2 = testColour(brightness * 0.6)
colour3 = testColour(brightness * 0.3)
# draw bands
pygame.draw.line(
image,
colour3,
(x - 1, position + Gel.BORDER),
(x + Gel.LANE_WIDTH + 1, position + Gel.BORDER),
)
pygame.draw.line(
image,
colour2,
(x, position + Gel.BORDER),
(x + Gel.LANE_WIDTH, position + Gel.BORDER),
)
pygame.draw.line(
image,
colour1,
(x + 1, position + Gel.BORDER),
(x + Gel.LANE_WIDTH - 1, position + Gel.BORDER),
)
# draw well
pygame.draw.rect(edges, edge_colour, (x, Gel.BORDER, Gel.LANE_WIDTH, Gel.LANE_HEIGHT), 1)
x += Gel.LANE_WIDTH + Gel.LANE_MARGIN
image.blit(edges, (0, 0))
return image
def _findDNAConcentrations(self, background):
"""Determines where in the concentration of DNA in every part of the gel"""
length = len(self.lanes[0])
for x in range(len(self.samples)):
for dna in self.samples[x]:
for y in range(Gel.LANE_HEIGHT - 2):
pos = int(dna["position"]) + y
if pos < length - 4:
# Very crude way to create blurred line
self.lanes[x][pos - 2] += 0.06 * dna["conc"] * dna["length"]
self.lanes[x][pos - 1] += 0.12 * dna["conc"] * dna["length"]
self.lanes[x][pos] += 0.2 * dna["conc"] * dna["length"]
self.lanes[x][pos + 1] += 0.12 * dna["conc"] * dna["length"]
self.lanes[x][pos + 2] += 0.06 * dna["conc"] * dna["length"]
def AgaroseGel(samples, *args, **kwargs):
myGel = Gel(size=(360, len(samples)), agarose=1.0)
for i, sample in enumerate(samples):
try:
sample = [(len(x), 100) for x in sample]
except:
pass
myGel.loadSample(1 + i, sample)
myGel.run(time=120)
my_image = myGel.expose(exposure=0.01)
pygame.image.save(my_image, "test_run.jpg")
webbrowser.open("test_run.jpg")
# display(360, 360, my_image)
# from PIL import Image
# img = Image.open('test_run.png')
# img.show()
# display(360, 360, my_image)
# import sys;sys.exit()
# Or save image as a PNG
# import os
# os.startfile('test_run.png')
if __name__ == "__main__":
from pydna import *
lambda_ = read("../tests/lambda.gb")
from Bio.Restriction import PstI
samples = sorted(lambda_.cut(PstI), key=len)
AgaroseGel(
[
samples,
]
)
LADDER_1KB = [
(300, 250),
(500, 150),
(700, 100),
(1000, 75),
(1500, 50),
(2000, 40),
(2500, 35),
(3000, 30),
(4000, 25),
(5000, 30),
(6000, 15),
(8000, 12),
(10000, 15),
(14000, 4),
(24000, 2),
]
# Samples are list of tuples in the form (length, concentration)
sample1 = [(400, 200), (500, 200), (900, 200)]
sample2 = [(400, 200), (900, 200), (1500, 200)]
sample3 = [(4000, 20), (4100, 20), (4900, 10)]
# Set up gel, giving its size and % agarose