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bug: permission issues when overwriting domains_color_file #41

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bug: permission issues when overwriting domains_color_file #41

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46 changes: 27 additions & 19 deletions ArrowerSVG.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@

import os
import sys
import shutil
from Bio import SeqIO
from random import uniform
from colorsys import hsv_to_rgb
Expand All @@ -27,27 +28,34 @@
gene_contour_thickness = 2 # thickness grows outwards
stripe_thickness = 3

domains_color_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), "domains_color_file.tsv")


source_domains_color_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), "domains_color_file.tsv")

def copy_color_domains_file_from_source(source_file):
home_dir = os.path.expanduser("~")
# Create the path to the .bigscape directory
bigscape_dir = os.path.join(home_dir, ".bigscape")
# Create the .bigscape directory if it doesn't exist
if not os.path.exists(bigscape_dir):
os.makedirs(bigscape_dir)
# Create the path to the file inside the .bigscape directory
domains_color_file = os.path.join(bigscape_dir, "domains_color_file.tsv")
if not os.path.isfile(domains_color_file):
shutil.copyfile(source_file, domains_color_file)
return domains_color_file

def read_color_domains_file():
# Try to read colors for domains
color_domains = {}

if os.path.isfile(domains_color_file):
print(" Found file with domains colors")
with open(domains_color_file, "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(domains_color_file, "a+")

domains_color_file = copy_color_domains_file_from_source(source_domains_color_file)
print(" Found file with domains colors")
with open(domains_color_file, "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)]
return color_domains


Expand Down Expand Up @@ -608,7 +616,7 @@ def SVG(write_html, outputfile, GenBankFile, BGCname, pfdFile, use_pfd, color_ge
#print(" Saving new color names for domains " + ", ".join(new_color_domains.keys()))
#else:
#print(" Saving new color names for 10+ domains")
domains_color_file = copy_color_domains_file_from_source(source_domains_color_file)
with open(domains_color_file, "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")
Expand Down