def generate_color_png(self, track_num, out_folder, imagemagick_path, log):
'''generation of color png based on tracks'''
out_folder = os.path.join(out_folder, "screenshots")
for strain in os.listdir(out_folder):
if os.path.isdir(os.path.join(out_folder, strain)):
for strand in ["forward", "reverse"]:
print("Running for {0}_{1}".format(strain, strand))
out_path = os.path.join(out_folder, strain, strand)
# convert original png to svg and give color on it.
log.write("Converting png file in {0} to svg.\n".format(
out_path))
log.write("Colorizing svg files.\n"
"Make sure the version of ImageMagick is "
"at least 6.9.0-0.\n")
for screenshot in os.listdir(out_path):
if screenshot.endswith(".png"):
print("Converting {0} to svg files and "
"Painting tracks now".format(
screenshot))
svg_file = screenshot.replace(".png", ".svg")
self._convert_svg(imagemagick_path, out_path,
screenshot, svg_file, log)
with open(os.path.join(
out_path, svg_file), "r") as f_h:
for line in f_h:
line = line.strip()
if line.startswith("<svg"):
line = line.split(" ")
height = line[-1].split("=")[-1][1:-2]
width = line[1].split("=")[-1][1:-1]
break
gen_svg(os.path.join(out_path, screenshot),
track_num, height, width)
log.write("All colorization for {0} is done.\n".format(out_path))
# convert to png file again
log.write("Converting svg file in {0} to png.\n".format(
out_path))
for screenshot in os.listdir(out_path):
if screenshot.endswith(".svg"):
print("Converting {0} to png files now...".format(
screenshot))
png_file = screenshot.replace(".svg", ".png")
self._convert_png(imagemagick_path, out_path,
screenshot, png_file, log)
Helper().remove_all_content(out_path, ".svg", "file")
log.write("All conversion for {0} is done.\n".format(out_path))
def generate_color_png(self, track_num, out_folder, imagemagick_path):
'''generation of color png based on tracks'''
out_folder = os.path.join(out_folder, "screenshots")
for strain in os.listdir(out_folder):
if os.path.isdir(os.path.join(out_folder, strain)):
for strand in ["forward", "reverse"]:
print("Running for {0}_{1}".format(strain, strand))
out_path = os.path.join(out_folder, strain, strand)
# convert original png to svg and give color on it.
for screenshot in os.listdir(out_path):
if screenshot.endswith(".png"):
print("convert {0} to svg and "
"painting tracks now...".format(screenshot))
svg_file = screenshot.replace(".png", ".svg")
self._convert_svg(imagemagick_path, out_path,
screenshot, svg_file)
with open(os.path.join(out_path, svg_file),
"r") as f_h:
for line in f_h:
line = line.strip()
if line.startswith("<svg"):
line = line.split(" ")
height = line[-1].split("=")[-1][1:-2]
width = line[1].split("=")[-1][1:-1]
break
gen_svg(os.path.join(out_path, screenshot),
track_num, height, width)
# convert to png file again
for screenshot in os.listdir(out_path):
if screenshot.endswith(".svg"):
print(
"convert {0} to png now...".format(screenshot))
png_file = screenshot.replace(".svg", ".png")
print(os.path.join(out_path, png_file))
self._convert_png(imagemagick_path, out_path,
screenshot, png_file)
Helper().remove_all_content(out_path, ".svg", "file")
def generate_color_png(self, track_num, out_folder, imagemagick_path):
out_folder = os.path.join(out_folder, "screenshots")
for strain in os.listdir(out_folder):
if os.path.isdir(os.path.join(out_folder, strain)):
for strand in ["forward", "reverse"]:
print("Running for {0}_{1}".format(strain, strand))
out_path = os.path.join(out_folder, strain, strand)
# convert original png to svg and give color on it.
for screenshot in os.listdir(out_path):
if screenshot.endswith(".png"):
print("convert {0} to svg and "
"painting tracks now...".format(
screenshot))
svg_file = screenshot.replace(".png", ".svg")
self._convert_svg(imagemagick_path, out_path,
screenshot, svg_file)
with open(os.path.join(
out_path, svg_file), "r") as f_h:
for line in f_h:
line = line.strip()
if line.startswith("<svg"):
line = line.split(" ")
height = line[-1].split("=")[-1][1:-2]
width = line[1].split("=")[-1][1:-1]
break
gen_svg(os.path.join(out_path, screenshot),
track_num, height, width)
# convert to png file again
for screenshot in os.listdir(out_path):
if screenshot.endswith(".svg"):
print("convert {0} to png now...".format(
screenshot))
png_file = screenshot.replace(".svg", ".png")
print(os.path.join(out_path, png_file))
self._convert_png(imagemagick_path, out_path,
screenshot, png_file)
Helper().remove_all_content(out_path, ".svg", "file")
def test_gen_svg(self):
gs.gen_svg("test_folder/test.png", 4, 1000, 400)
data = import_data("test_folder/test.svg")
self.assertEqual("\n".join(data), self.example.svg)
def test_gen_svg(self):
gs.gen_svg("test_folder/test.png", 4, 1000, 400)
data = import_data("test_folder/test.svg")
self.assertEqual("\n".join(data), self.example.svg)