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ArrowerSVG.py
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ArrowerSVG.py
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#! /usr/bin/python
######################################################################
# #
# PLOT ARROWS FOR GENE CLUSTER GIVEN A GenBank FILE #
# Peter Cimermancic #
# April 2010 #
# heavily modified by Jorge Navarro 2016 #
######################################################################
import os
from pathlib import Path
import sys
from Bio import SeqIO
from random import uniform
from colorsys import hsv_to_rgb
from colorsys import rgb_to_hsv
from math import sin, atan2, pi
from collections import defaultdict
global internal_domain_margin
global gene_contour_thickness
global stripe_thickness
global gene_categories_color
internal_domain_margin = 3
domain_contour_thickness = 1
gene_contour_thickness = 2 # thickness grows outwards
stripe_thickness = 3
def read_color_domains_file(output_folder):
# Try to read colors for domains
color_domains = {}
if os.path.isfile(output_folder / Path("domains_color_file.tsv")):
print(" Found file with domains colors")
with open(output_folder / Path("domains_color_file.tsv"), "r") as color_domains_handle:
for line in color_domains_handle:
# handle comments and empty lines
if line[0] != "#" and line.strip():
row = line.strip().split("\t")
name = row[0]
rgb = row[1].split(",")
color_domains[name] = [int(rgb[x]) for x in range(3)]
else:
print(" Domains colors file was not found. An empty file will be created")
color_domains_handle = open(output_folder / Path("domains_color_file.tsv"), "a+")
return color_domains
# --- Draw arrow for gene
def draw_arrow(additional_tabs, X, Y, L, l, H, h, strand, color, color_contour, category, gid, domain_list):
"""
SVG code for arrow:
- (X,Y) ... upper left (+) or right (-) corner of the arrow
- L ... arrow length
- H ... arrow height
- strand
- h ... arrow head edge width
- l ... arrow head length
- color
- strand
the edges are ABCDEFG starting from (X,Y)
"""
if strand == '+':
head_end = L
if L < l:
# squeeze arrow if length shorter than head length
A = [X,Y-h]
B = [X+L,Y+H/2]
C = [X,Y+H+h]
head_start = 0
points = [A, B, C]
else:
A = [X,Y]
B = [X+L-l,Y]
C = [X+L-l,Y-h]
D = [X+L,Y+H/2]
E = [X+L-l,Y+H+h]
F = [X+L-l,Y+H]
G = [X,Y+H]
head_start = L - l # relative to the start of the gene, not absolute coords.
points = [A, B, C, D, E, F, G]
elif strand == '-':
head_start = 0
if L < l:
# squeeze arrow if length shorter than head length
A = [X,Y+H/2]
B = [X+L,Y-h]
C = [X+L,Y+H+h]
head_end = L
points = [A, B, C]
else:
A = [X+L,Y]
B = [X+l,Y]
C = [X+l,Y-h]
D = [X,Y+H/2]
E = [X+l,Y+H+h]
F = [X+l,Y+H]
G = [X+L,Y+H]
head_end = l
points = [A, B, C, D, E, F, G]
else:
return ""
head_length = head_end - head_start
if head_length == 0:
return ""
points_coords = []
for point in points:
points_coords.append(str(int(point[0])) + "," + str(int(point[1])))
arrow = additional_tabs + "\t<g>\n"
# unidentified genes don't have a title and have a darker contour
if gid != "NoName":
arrow += additional_tabs + "\t\t<title>" + gid + "</title>\n"
else:
color_contour = [50, 50, 50]
arrow += "{}\t\t<polygon class=\"{}\" ".format(additional_tabs, gid)
arrow += "points=\"{}\" fill=\"rgb({})\" ".format(" ".join(points_coords), ",".join([str(val) for val in color]))
arrow += "fill-opacity=\"1.0\" stroke=\"rgb({})\" ".format(",".join([str(val) for val in color_contour]))
arrow += "stroke-width=\"{}\" {} />\n".format(str(gene_contour_thickness), category)
# paint domains. Domains on the tip of the arrow should not have corners sticking
# out of them
for domain in domain_list:
#[X, L, H, domain_accession, (domain_name, domain_description), color, color_contour]
dX = domain[0]
dL = domain[1]
dH = domain[2]
dacc = domain[3]
dname = domain[4][0]
ddesc = domain[4][1]
dcolor = domain[5]
dccolour = domain[6]
arrow += additional_tabs + "\t\t<g>\n"
arrow += "{}\t\t\t<title>{} ({})\n\"{}\"</title>\n".format(additional_tabs, dname, dacc, ddesc)
if strand == "+":
# calculate how far from head_start we (the horizontal guide at y=Y+internal_domain_margin)
# would crash with the slope
# Using similar triangles:
collision_x = head_length * (h + internal_domain_margin)
collision_x /= (h + H/2.0)
collision_x = round(collision_x)
# either option for x_margin_offset work
#m = -float(h + H/2)/(head_length) #slope of right line
#x_margin_offset = (internal_domain_margin*sqrt(1+m*m))/m
#x_margin_offset = -(x_margin_offset)
x_margin_offset = internal_domain_margin/sin(pi - atan2(h+H/2.0,-head_length))
if (dX + dL) < head_start + collision_x - x_margin_offset:
arrow += "{}\t\t\t<rect class=\"{}\" x=\"{}\" ".format(additional_tabs, dacc, str(X+dX))
arrow += "y=\"{}\" stroke-linejoin=\"round\" ".format(str(Y + internal_domain_margin))
arrow += "width=\"{}\" height=\"{}\" ".format(str(dL), str(dH))
arrow += "fill=\"rgb({})\" stroke=\"rgb({})\" ".format(",".join([str(val) for val in dcolor]), ",".join([str(val) for val in dccolour]))
arrow += "stroke-width=\"{}\" opacity=\"0.75\" />\n".format(str(domain_contour_thickness))
else:
del points[:]
if dX < head_start + collision_x - x_margin_offset:
# add points A and B
points.append([X + dX, Y + internal_domain_margin])
points.append([X + head_start + collision_x - x_margin_offset, Y + internal_domain_margin])
else:
# add point A'
start_y_offset = (h + H/2)*(L - x_margin_offset - dX)
start_y_offset /= head_length
start_y_offset = int(start_y_offset)
points.append([X + dX, int(Y + H/2 - start_y_offset)])
# handle the rightmost part of the domain
if dX + dL >= head_end - x_margin_offset: # could happen more easily with the scaling
points.append([X + head_end - x_margin_offset, int(Y + H/2)]) # right part is a triangle
else:
# add points C and D
end_y_offset = (2*h + H)*(L - x_margin_offset - dX - dL)
end_y_offset /= 2*head_length
end_y_offset = int(end_y_offset)
points.append([X + dX + dL, int(Y + H/2 - end_y_offset)])
points.append([X + dX + dL, int(Y + H/2 + end_y_offset)])
# handle lower part
if dX < head_start + collision_x - x_margin_offset:
# add points E and F
points.append([X + head_start + collision_x - x_margin_offset, Y + H - internal_domain_margin])
points.append([X + dX, Y + H - internal_domain_margin])
else:
# add point F'
points.append([X + dX, int(Y + H/2 + start_y_offset)])
del points_coords[:]
for point in points:
points_coords.append(str(int(point[0])) + "," + str(int(point[1])))
arrow += "{}\t\t\t<polygon class=\"{}\" ".format(additional_tabs, dacc)
arrow += "points=\"{}\" stroke-linejoin=\"round\" ".format(" ".join(points_coords))
arrow += "width=\"{}\" height=\"{}\" ".format(str(dL), str(dH))
arrow += "fill=\"rgb({})\" ".format(",".join([str(val) for val in dcolor]))
arrow += "stroke=\"rgb({})\" ".format(",".join([str(val) for val in dccolour]))
arrow += "stroke-width=\"{}\" opacity=\"0.75\" />\n".format(str(domain_contour_thickness))
# now check other direction
else:
# calculate how far from head_start we (the horizontal guide at y=Y+internal_domain_margin)
# would crash with the slope
# Using similar triangles:
collision_x = head_length * ((H/2) - internal_domain_margin)
collision_x /= (h + H/2.0)
collision_x = round(collision_x)
x_margin_offset = round(internal_domain_margin/sin(atan2(h+H/2.0,head_length)))
# nice, blocky domains
if dX > collision_x + x_margin_offset:
arrow += "{}\t\t\t<rect class=\"{}\" ".format(additional_tabs, dacc)
arrow += "x=\"{}\" y=\"{}\" ".format(str(X+dX), str(Y + internal_domain_margin))
arrow += "stroke-linejoin=\"round\" width=\"{}\" height=\"{}\" ".format(str(dL), str(dH))
arrow += "fill=\"rgb({})\" ".format(",".join([str(val) for val in dcolor]))
arrow += "stroke=\"rgb({})\" ".format(",".join([str(val) for val in dccolour]))
arrow += "stroke-width=\"{}\" opacity=\"0.75\" />\n".format(str(domain_contour_thickness))
else:
del points[:]
# handle lefthand side. Regular point or pointy start?
if dX >= x_margin_offset:
start_y_offset = round((h + H/2)*(dX - x_margin_offset)/head_length)
points.append([X + dX, Y + H/2 - start_y_offset])
else:
points.append([X + x_margin_offset, Y + H/2])
# handle middle/end
if dX + dL < collision_x + x_margin_offset:
if head_length != 0:
end_y_offset = round((h + H/2)*(dX + dL - x_margin_offset)/head_length)
else:
end_y_offset = 0
points.append([X + dX + dL, Y + H/2 - end_y_offset])
points.append([X + dX + dL, Y + H/2 + end_y_offset])
else:
points.append([X + collision_x + x_margin_offset, Y + internal_domain_margin])
points.append([X + dX + dL, Y + internal_domain_margin])
points.append([X + dX + dL, Y + internal_domain_margin + dH])
points.append([X + collision_x + x_margin_offset, Y + internal_domain_margin + dH])
# last point, if it's not a pointy domain
if dX >= x_margin_offset:
points.append([X + dX, Y + H/2 + start_y_offset])
del points_coords[:]
for point in points:
points_coords.append(str(int(point[0])) + "," + str(int(point[1])))
arrow += "{}\t\t\t<polygon class=\"{}\" ".format(additional_tabs, dacc)
arrow += "points=\"{}\" stroke-linejoin=\"round\" ".format(" ".join(points_coords))
arrow += "width=\"{}\" height=\"{}\" ".format(str(dL), str(dH))
arrow += "fill=\"rgb({})\" ".format(",".join([str(val) for val in dcolor]))
arrow += "stroke=\"rgb({})\" ".format(",".join([str(val) for val in dccolour]))
arrow += "stroke-width=\"{}\" opacity=\"0.75\" />\n".format(str(domain_contour_thickness))
arrow += additional_tabs + "\t\t</g>\n"
arrow += additional_tabs + "\t</g>\n"
return arrow
def draw_line(X,Y,L):
"""
Draw a line below genes
"""
line = "<line x1=\"{}\" y1=\"{}\" x2=\"{}\" y2=\"{}\" style=\"stroke:rgb(70,70,70); stroke-width:{} \"/>\n".format(str(X), str(Y), str(X+L), str(Y), str(stripe_thickness))
return line
def new_color(gene_or_domain):
# see https://en.wikipedia.org/wiki/HSL_and_HSV
# and http://stackoverflow.com/a/1586291
h = uniform(0, 1) # all possible colors
if gene_or_domain == "gene":
s = uniform(0.15, 0.3)
v = uniform(0.98, 1.0)
elif gene_or_domain == "domain":
s = uniform(0.5, 0.75) # lower: less saturated
v = uniform(0.7, 0.9) # lower = darker
else:
sys.exit("unknown kind of color. Should be 'gene' or 'domain'")
r, g, b = tuple(int(c * 255) for c in hsv_to_rgb(h, s, v))
return [r, g, b]
def SVG(output_folder, write_html, outputfile, GenBankFile, BGCname, pfdFile, use_pfd, color_genes, color_domains, pfam_domain_categories, pfam_info, loci, max_width, H=30, h=15, l=30, mX=10, mY=10, scaling=30, absolute_start=0, absolute_end=-1):
'''
Create the main SVG document:
- read pfd file with domain information (pfdFile contains complete path)
- read GenBank document (GenBankFile contains handle of opened file)
- record genes, start and stop positions, and strands, and associate domains
- write the SVG files
'''
# for colors not found in colors_genes and color_domains, we need to generate them from scratch
new_color_genes = {}
new_color_domains = {}
SVG_TEXT = "" # here we keep all the text that will be written down as a file
# check whether we have a corresponding pfd file wih domain annotations
if use_pfd:
if not os.path.isfile(pfdFile):
sys.exit("Error (Arrower): " + pfdFile + " not found")
# --- create SVG header. We have to get max_width first
# This means that we have to read the gbk file once to know num loci, max_width
if loci == -1:
try:
records = list(SeqIO.parse(GenBankFile), "genbank")
except:
sys.exit(" Arrower: error while opening GenBank")
else:
loci = len(records)
max_width = 0
for record in records:
if len(record) > max_width:
max_width = len(record)
if absolute_end < 0: # absolute_end == -1 means "the whole region"
absolute_end = max_width
else:
if (absolute_end - absolute_start) < max_width: # user specified something shorter than full region
max_width = float(absolute_end - absolute_start)
else: # user specified something bigger than full region. Cropping to max_width
absolute_end = max_width
max_width /= scaling
if write_html:
header = "\t\t<div title=\"" + BGCname + "\">\n"
additional_tabs = "\t\t\t"
header += "{}<svg width=\"{}\" height=\"{}\">\n".format(additional_tabs, str(max_width + 2*(mX)), str(loci*(2*h + H + 2*mY)))
addY = loci*(2*h + H + 2*mY)
else:
header = "<svg version=\"1.1\" baseProfile=\"full\" xmlns=\"http://www.w3.org/2000/svg\" width=\"" + str(max_width + 2*(mX)) + "\" height=\"" + str(loci*(2*h + H + 2*mY)) + "\">\n"
addY = 0
additional_tabs = "\t"
SVG_TEXT = header
# For info on the color matrix definition:
# https://www.w3.org/TR/SVG11/filters.html#feColorMatrixElement
# Core Bio: "#DC143C", (220, 20, 60) Dark red
# Other Bio:
# original: "#DF809D", (223, 128, 157) Pink .87, 0.5, 0.61
# alternative: #f4a236, (244,162,54) 0.95, 0.63, 0.21
# Transporter: "#3F9FBA" (63, 159, 186) Blue
# 32839a, (50, 131, 154), 0.19, 0.51, 0.6
# Regulator: "#63BB6D" (99, 187, 109) Green
# #127E1B, (18,126,27) 0.07, 0.49, 0.1
if len(pfam_domain_categories) > 0:
filters = additional_tabs + "<filter id=\"shadow_CoreBio\" color-interpolation-filters=\"sRGB\" x=\"-65%\" y=\"-25%\" width=\"230%\" height=\"150%\">\n"
filters += additional_tabs + "\t<feColorMatrix in=\"SourceGraphic\" result=\"matrixOut\" type=\"matrix\" values=\"0 0 0 0 0.85 0 0 0 0 0.08 0 0 0 0 0.23 0 0 0 1 0\" />\n"
filters += additional_tabs + "\t<feGaussianBlur in=\"matrixOut\" result=\"blurOut\" stdDeviation=\"7\" />\n"
filters += additional_tabs + "\t<feBlend in=\"SourceGraphic\" in2=\"blurOut\" mode=\"normal\" />\n"
filters += additional_tabs + "</filter>\n"
filters += additional_tabs + "<filter id=\"shadow_OtherBio\" color-interpolation-filters=\"sRGB\" x=\"-65%\" y=\"-25%\" width=\"230%\" height=\"150%\">\n"
filters += additional_tabs + "\t<feColorMatrix in=\"SourceGraphic\" result=\"matrixOut\" type=\"matrix\" values=\"0 0 0 0 0.95 0 0 0 0 0.63 0 0 0 0 0.21 0 0 0 1 0\" />\n"
filters += additional_tabs + "\t<feGaussianBlur in=\"matrixOut\" result=\"blurOut\" stdDeviation=\"7\" />\n"
filters += additional_tabs + "\t<feBlend in=\"SourceGraphic\" in2=\"blurOut\" mode=\"normal\" />\n"
filters += additional_tabs + "</filter>\n"
filters += additional_tabs + "<filter id=\"shadow_Transporter\" color-interpolation-filters=\"sRGB\" x=\"-65%\" y=\"-25%\" width=\"230%\" height=\"150%\">\n"
filters += additional_tabs + "\t<feColorMatrix in=\"SourceGraphic\" result=\"matrixOut\" type=\"matrix\" values=\"0 0 0 0 0.19 0 0 0 0 0.51 0 0 0 0 0.6 0 0 0 1 0\" />\n"
filters += additional_tabs + "\t<feGaussianBlur in=\"matrixOut\" result=\"blurOut\" stdDeviation=\"7\" />\n"
filters += additional_tabs + "\t<feBlend in=\"SourceGraphic\" in2=\"blurOut\" mode=\"normal\" />\n"
filters += additional_tabs + "</filter>\n"
filters += additional_tabs + "<filter id=\"shadow_Regulator\" color-interpolation-filters=\"sRGB\" x=\"-65%\" y=\"-25%\" width=\"230%\" height=\"150%\">\n"
filters += additional_tabs + "\t<feColorMatrix in=\"SourceGraphic\" result=\"matrixOut\" type=\"matrix\" values=\"0 0 0 0 0.07 0 0 0 0 0.49 0 0 0 0 0.1 0 0 0 1 0\" />\n"
filters += additional_tabs + "\t<feGaussianBlur in=\"matrixOut\" result=\"blurOut\" stdDeviation=\"7\" />\n"
filters += additional_tabs + "\t<feBlend in=\"SourceGraphic\" in2=\"blurOut\" mode=\"normal\" />\n"
filters += additional_tabs + "</filter>\n"
SVG_TEXT += filters
# --- read in GenBank file
# handle domains
if use_pfd:
identifiers = defaultdict(list)
with open(pfdFile, "r") as pfd_handle:
for line in pfd_handle:
row = line.strip().split("\t")
# use to access to parent's properties
identifier = row[9].replace("<","").replace(">","")
# if it's the new version of pfd file, we can take the last part
# to make it equal to the identifiers used in gene_list. Strand
# is recorded in parent gene anyway
if ":strand:+" in identifier:
identifier = identifier.replace(":strand:+", "")
strand = "+"
if ":strand:-" in identifier:
identifier = identifier.replace(":strand:-", "")
strand = "-"
width = 3*(int(row[4]) - int(row[3]))
if strand == "+":
# multiply by 3 because the env. coordinate is in aminoacids, not in bp
# This start is relative to the start of the gene
start = 3*int(row[3])
else:
loci_start = int(row[7].replace("<","").replace(">",""))
loci_end = int(row[8].replace("<","").replace(">",""))
start = loci_end - loci_start - 3*int(row[3]) - width
# geometry
start = int(start/scaling)
width = int(width/scaling)
# accession
domain_acc = row[5].split(".")[0]
# colors
try:
color = color_domains[domain_acc]
except KeyError:
color = new_color("domain")
new_color_domains[domain_acc] = color
color_domains[domain_acc] = color
pass
# contour color is a bit darker. We go to h,s,v space for that
h_, s, v = rgb_to_hsv(float(color[0])/255.0, float(color[1])/255.0, float(color[2])/255.0)
color_contour = tuple(int(c * 255) for c in hsv_to_rgb(h_, s, 0.8*v))
# [X, L, H, domain_acc, color, color_contour]
identifiers[identifier].append([start, width, int(H - 2*internal_domain_margin), domain_acc, pfam_info[domain_acc], color, color_contour])
loci = 0
feature_counter = 1
records = list(SeqIO.parse(GenBankFile, "genbank"))
for seq_record in records:
add_origin_Y = loci * (2*(h+mY) + H)
# draw a line that coresponds to cluster size
ClusterSize = len(seq_record.seq)
if (absolute_end - absolute_start) < ClusterSize:
ClusterSize = (absolute_end - absolute_start)
line = draw_line(mX, add_origin_Y + mY + h + H/2, ClusterSize/scaling)
SVG_TEXT += additional_tabs + "<g>\n"
SVG_TEXT += additional_tabs + "\t" + line
# Calculate features for all arrows
for feature in [feature for feature in seq_record.features if feature.location.start >= absolute_start and feature.location.end <= absolute_end]:
if feature.type == 'CDS':
# Get name
try:
GeneName = feature.qualifiers['gene'][0]
cds_tag = GeneName
except KeyError:
GeneName = 'NoName'
cds_tag = ""
if "locus_tag" in feature.qualifiers:
cds_tag += " (" + feature.qualifiers["locus_tag"][0] + ")"
if "product" in feature.qualifiers:
cds_tag += "\n" + feature.qualifiers["product"][0]
# Get color
color = (255,255,255)
#try:
#color = color_genes[GeneName]
#except KeyError:
#color = new_color("gene")
#new_color_genes[GeneName] = color
#color_genes[GeneName] = color
#pass
color_contour = (0,0,0)
# change to hsv color palette to lower shade for contour color
#h_, s, v = rgb_to_hsv(float(color[0])/255.0, float(color[1])/255.0, float(color[2])/255.0)
#color_contour = tuple(int(c * 255) for c in hsv_to_rgb(h_, s, 0.4*v))
# Get strand
strand = feature.strand
if strand == -1:
strand = '-'
elif strand == 1:
strand = '+'
else:
sys.exit("Weird strand value: " + strand)
# define arrow's start and end
# http://biopython.org/DIST/docs/api/Bio.SeqFeature.FeatureLocation-class.html#start
start = feature.location.start - absolute_start
start = int(start/scaling)
stop = feature.location.end - absolute_start
stop = int(stop/scaling)
# assemble identifier to match domains with this feature
try:
protein_id = feature.qualifiers['protein_id'][0]
except KeyError:
protein_id = ""
pass
identifier = BGCname + "_ORF" + str(feature_counter)
identifier += ":gid::" if GeneName == "NoName" else ":gid:" + str(GeneName) + ":"
identifier += "pid:" + str(protein_id) + ":loc:" + str(feature.location.start) + ":" + str(feature.location.end)
identifier = identifier.replace("<","").replace(">","")
# gene category according to domain content
#has_core = False
#has_otherbio = False
#has_transporter = False
#has_regulator = False
#for row in identifiers[identifier]:
#dom_acc = row[3]
#cat = ""
#try:
#cat = pfam_domain_categories[dom_acc]
#except KeyError:
#pass
#if cat == "Core Biosynthetic":
#has_core = True
#if cat == "Other Biosynthetic":
#has_otherbio = True
#if cat == "Transporter":
#has_transporter = True
#if cat == "Regulator":
#has_regulator = True
gene_category = ""
#if has_core:
#gene_category = "filter=\"url(#shadow_CoreBio)\""
#if has_otherbio and not (has_core or has_transporter or has_regulator):
#gene_category = "filter=\"url(#shadow_OtherBio)\""
#if has_transporter and not (has_core or has_otherbio or has_regulator):
#gene_category = "filter=\"url(#shadow_Transporter)\""
#if has_regulator and not (has_core or has_otherbio or has_transporter):
#gene_category = "filter=\"url(#shadow_Regulator)\""
#X, Y, L, l, H, h, strand, color, color_contour, category, gid, domain_list
arrow = draw_arrow(additional_tabs, start+mX, add_origin_Y+mY+h, int(feature.location.end-feature.location.start)/scaling, l, H, h, strand, color, color_contour, gene_category, cds_tag, identifiers[identifier])
if arrow == "":
print(" (ArrowerSVG) Warning: something went wrong with {}".format(BGCname))
SVG_TEXT += arrow
feature_counter += 1
loci += 1
SVG_TEXT += additional_tabs + "</g>\n"
SVG_TEXT += additional_tabs[:-2] + "</svg>\n"
if write_html:
SVG_TEXT += "\t\t</div>\n"
# finally append new colors to file:
#if len(new_color_genes) > 0:
#if len(new_color_genes) < 10:
#print(" Saving new color names for genes " + ", ".join(new_color_genes.keys()))
#else:
#print(" Saving new color names for 10+ genes...")
#with open(gene_color_file, "a") as color_genes_handle:
#for new_names in new_color_genes:
#color_genes_handle.write(new_names + "\t" + ",".join([str(ncg) for ncg in new_color_genes[new_names]]) + "\n")
if len(new_color_domains) > 0:
#if len(new_color_domains) < 10:
#print(" Saving new color names for domains " + ", ".join(new_color_domains.keys()))
#else:
#print(" Saving new color names for 10+ domains")
with open(output_folder / Path("domains_color_file.tsv"), "a") as color_domains_handle:
for new_names in new_color_domains:
color_domains_handle.write(new_names + "\t" + ",".join([str(ncdom) for ncdom in new_color_domains[new_names]]) + "\n")
mode = "a" if write_html == True else "w"
with open(outputfile, mode) as handle:
handle.write(SVG_TEXT)