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Update uphyloplot2.py #22

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Update uphyloplot2.py #22

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72 changes: 38 additions & 34 deletions uphyloplot2.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#!/usr/bin/env python
# Stefan Kurtenbach
# [email protected]
# Stefan Kurtenbach, edited by Andrew Erickson
# [email protected], edited by [email protected]
def main():
version = "2.3"
print("uphyloplot2 version " + version)
Expand Down Expand Up @@ -162,43 +162,46 @@ def draw_circle(x_coord, y_coord):
input_data = list(reader)

longest_tree = 0

for data_row in input_data:
if len(data_row[0].split(".")) > longest_tree:
if data_row and len(data_row[0].split(".")) > longest_tree:
longest_tree = len(data_row[0].split("."))

for step in range(longest_tree): # first circle is already placed
next_circles = []

for data_row in input_data:
if len(data_row[0].split(".")) == step + 2: # if one of the next circles (starts with 1.1, 1.2 for ==step+2
for current_circle in current_circles:
if data_row[0][:len(str(current_circle[0]))] == str(current_circle[0]): # is that a subsequent circle?
if step == 0: current_angle = 60
else: current_angle = angle_of_subclones
for iteration in range(current_circle[3]): # define which angle
if current_angle < 0:
current_angle -= angle_of_subclones
current_angle *= -1
current_circle[3] += 1

delta_x = ((math.sin(math.radians(current_angle))) * (float(data_row[1]) * scale_factor_data + additional_space_between_circles)) * overall_scale_factor
delta_y = ((math.cos(math.radians(current_angle))) * (float(data_row[1]) * scale_factor_data + additional_space_between_circles)) * overall_scale_factor

output.append(draw_rect(current_circle[1], current_circle[2], float(data_row[1]) * scale_factor_data + additional_space_between_circles, 100, current_angle, colors[current_color]))
current_color += 1
output.append(draw_circle(current_circle[1] + delta_x, current_circle[2] + delta_y))
next_circles.append([data_row[0], current_circle[1] + delta_x, current_circle[2] + delta_y, 0])


text = str(data_row[0])
for rownr, row in enumerate(input_data):
if row[0] == text:
text = ABC[rownr]
if [row[0], text] not in clones_IDs:
clones_IDs.append([row[0], text])
break
output.append('''<text text-anchor='middle' ><tspan x="''' + str(current_circle[1] + delta_x + start_pos[0] + plot_nr * space_between_plots) + '''" y="''' + str(current_circle[2] + delta_y + start_pos[1] + 15 + 3) + '''" font-family="'ArialMT'" font-size="8">''' + text + '''</tspan>''')
output.append("</text>")
if data_row: # check if data_row is not empty
if len(data_row[0].split(".")) == step + 2: # if one of the next circles (starts with 1.1, 1.2 for ==step+2
for current_circle in current_circles:
if data_row[0][:len(str(current_circle[0]))] == str(current_circle[0]): # is that a subsequent circle?
if step == 0: current_angle = 60
else: current_angle = angle_of_subclones
for iteration in range(current_circle[3]): # define which angle
if current_angle < 0:
current_angle -= angle_of_subclones
current_angle *= -1
current_circle[3] += 1

delta_x = ((math.sin(math.radians(current_angle))) * (float(data_row[1]) * scale_factor_data + additional_space_between_circles)) * overall_scale_factor
delta_y = ((math.cos(math.radians(current_angle))) * (float(data_row[1]) * scale_factor_data + additional_space_between_circles)) * overall_scale_factor

output.append(draw_rect(current_circle[1], current_circle[2], float(data_row[1]) * scale_factor_data + additional_space_between_circles, 100, current_angle, colors[current_color]))
current_color += 1
output.append(draw_circle(current_circle[1] + delta_x, current_circle[2] + delta_y))
next_circles.append([data_row[0], current_circle[1] + delta_x, current_circle[2] + delta_y, 0])


text = str(data_row[0])
for rownr, row in enumerate(input_data):
if row:
if row[0] == text:
text = ABC[rownr]
if [row[0], text] not in clones_IDs:
clones_IDs.append([row[0], text])
break
output.append('''<text text-anchor='middle' ><tspan x="''' + str(current_circle[1] + delta_x + start_pos[0] + plot_nr * space_between_plots) + '''" y="''' + str(current_circle[2] + delta_y + start_pos[1] + 15 + 3) + '''" font-family="'ArialMT'" font-size="8">''' + text + '''</tspan>''')
output.append("</text>")
current_circles = copy.copy(next_circles)


Expand All @@ -225,8 +228,9 @@ def draw_circle(x_coord, y_coord):
input_data = list(reader)
for x, i in enumerate(input_data):
for p, q in enumerate(clones_IDs):
if i[0] == q[0]:
input_data[x].append(clones_IDs[p][1])
if len(i) > 0 and len(q) > 0:
if i[0] == q[0]:
input_data[x].append(clones_IDs[p][1])

with open("./CNV_files/"+working_file, mode='w') as output:
writer = csv.writer(output, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
Expand Down