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b4bd946 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 | import drawsvg as draw
import numpy as np
def draw_line(d,x1,y1,x2,y2,color):
d.append(draw.Lines(x1,y1,
x2,y2,
close=False,
fill="none",
stroke=color,
stroke_width=2))
def draw_nucleotide(d,x, y, nt, color):
""" Draw one nucleotide in a circle
"""
assert(len(nt)==1)
d.append(draw.Circle(x, y, 8,
fill=color, stroke_width=2, stroke='black'))
deltax = 4.3 if nt=="A" else (4.5 if nt=="U" else 4.7)
d.append(draw.Text(nt, 11, x-deltax, y+4, fill="black", font_weight="bold")) # use 11pt text
def draw_oligo(d,xs, ys, nts, colors):
lastx = None
lasty = None
for (x,y,nt,color) in zip(xs,ys,nts,colors): # first draw all the black lines connecting the nucleotides
if lastx != None:
draw_line(d,lastx,lasty,x,y,"black")
lastx, lasty = x,y
for (x,y,nt,color) in zip(xs,ys,nts,colors):
draw_nucleotide(d,x,y,nt,color)
BASE_PAIR_COLOR = "#ff4e4e"
DELTA_X = 20
DELTA_Y = 20
LOOP_RADIUS_PER_LOOP_LENGTH = {3:18, 4:20, 5:23,6:26}
def draw_stem_loop(nts, stem_length, colors, filename):
""" First nucleotide is just upstream of stem; then stem; then loop; then 3' part of stem; then another nucleotide outside stem
"""
assert(len(nts)==len(colors))
d = draw.Drawing(500, 200, origin='center')
for i in range(stem_length):
draw_line(d,i*DELTA_X,0,i*DELTA_X,DELTA_Y,BASE_PAIR_COLOR)
loop_length = len(nts) - 2*stem_length - 2
assert((loop_length >= 3) and (loop_length <= 6))
loop_radius = LOOP_RADIUS_PER_LOOP_LENGTH[loop_length]
xs = [-0.7*DELTA_X,] + [DELTA_X * i for i in range(stem_length)] + [DELTA_X * (stem_length-1) + loop_radius* np.cos(2*np.pi*(1/2)/(loop_length+2)) - loop_radius * np.cos(2*np.pi*(i+3/2)/(loop_length+2)) for i in range(loop_length)] + [DELTA_X * (stem_length-1-i) for i in range(stem_length)] + [-0.7*DELTA_X]
ys = [-0.7*DELTA_Y,] + [0] * stem_length + [DELTA_Y/2 - loop_radius * np.sin(2*np.pi*(i+3/2)/(loop_length+2)) for i in range(loop_length)] + [DELTA_Y]*stem_length + [1.7*DELTA_Y]
draw_oligo(d,xs,ys,nts,colors)
d.set_pixel_scale(2) # Set number of pixels per geometry unit
d.save_svg(filename)
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