Skip to content

Commit

Permalink
Update to check for rsvg-convert, fixes issue #1
Browse files Browse the repository at this point in the history
  • Loading branch information
@ar0ch
ar0ch committed Dec 2, 2019
1 parent 430e0b0 commit c5d0016
Show file tree
Hide file tree
Showing 4 changed files with 57 additions and 15 deletions.
Binary file added example_ideogram/example.pdf
View file
Binary file not shown.
2 changes: 1 addition & 1 deletion setup.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@

setuptools.setup(
name="tagore",
version="1.0.1",
version="1.0.2",
author="Applied Bioinformatics Laboratory",
author_email="abil@ihrc.com",
description="A simple way to visualize features on human chromosome ideograms",
Expand Down
35 changes: 28 additions & 7 deletions tagore
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ import sys
from argparse import ArgumentParser, HelpFormatter


VERSION = '1.0.1'
VERSION = '1.0.2'

COORDINATES = {
"1": {"cx": 128.6, "cy": 1.5, "ht": 1654.5, "width": 118.6},
Expand Down Expand Up @@ -203,6 +203,9 @@ if __name__ == "__main__":
PARSER.add_argument('-f', '--force', required=False, default=False,
help="Overwrite output files if they exist already",
action="store_true")
PARSER.add_argument('-ofmt', '--oformat', required=False, default='png',
help="Output format for conversion (pdf requires rsvg-convert)",
metavar='[png/pdf]')
PARSER.add_argument('-v', '--verbose', required=False, default=False,
help="Display verbose output",
action="store_true")
Expand All @@ -214,9 +217,21 @@ if __name__ == "__main__":
if ARGS.build not in ['hg37', 'hg38']:
print(f"\033[91mBuild must be either 'hg37' or 'hg38', you supplied {ARGS.build}.\033[0m")
sys.exit()
if shutil.which("rsvg", mode=os.X_OK) is None:
print(f"\033[91mCould not find `rsvg` in PATH.\033[0m")
sys.exit()

if shutil.which("rsvg-convert", mode=os.X_OK) is None:
if shutil.which("rsvg", mode=os.X_OK) is None:
print(f"\033[91mCould not find `rsvg` or `rsvg-convert` in PATH.\033[0m")
sys.exit()
else:
RSVG = True
if ARGS.oformat != "png":
print(f"\033[93m`rsvg` only supports PNG output, using png\033[0m")
ARGS.oformat = "png"
else:
RSVG = False
if ARGS.oformat not in ["png", "pdf"]:
print(f"\033[93m{ARGS.oformat} is not PNG or PDF, using PNG\033[0m")
ARGS.oformat = "png"
BASE_PATH = os.path.join(sys.prefix, 'lib', 'tagore-data', 'base.svg.p')
try:
BASE = open(BASE_PATH, 'rb')
Expand All @@ -236,11 +251,17 @@ if __name__ == "__main__":
else:
printif(f"\033[94mSaving to: {ARGS.prefix}.svg\033[0m", ARGS.verbose)
draw(ARGS)
printif(f"\033[94mConverting {ARGS.prefix}.svg -> {ARGS.prefix}.png\033[0m", ARGS.verbose)
printif(f"\033[94mConverting {ARGS.prefix}.svg -> {ARGS.prefix}.{ARGS.oformat} \033[0m",
ARGS.verbose)
try:
subprocess.check_output(f"rsvg {ARGS.prefix}.svg {ARGS.prefix}.png", shell=True)
if RSVG:
subprocess.check_output(f"rsvg {ARGS.prefix}.svg {ARGS.prefix}.{ARGS.oformat} ",
shell=True)
else:
subprocess.check_output(f"rsvg-convert -o {ARGS.prefix}.{ARGS.oformat} -f {ARGS.oformat} {ARGS.prefix}.svg ", shell=True)
except subprocess.CalledProcessError as rsvg_e:
printif(f"\033[91mFailed SVG to PNG conversion...\033[0m", ARGS.verbose)
raise rsvg_e
finally:
printif(f"\033[92mSuccessfully converted SVG to PNG\033[0m", ARGS.verbose)
printif(f"\033[92mSuccessfully converted SVG to {ARGS.oformat.upper()}\033[0m",
ARGS.verbose)
35 changes: 28 additions & 7 deletions tagore.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
from argparse import ArgumentParser, HelpFormatter


VERSION = '1.0.1'
VERSION = '1.0.2'

COORDINATES = {
"1": {"cx": 128.6, "cy": 1.5, "ht": 1654.5, "width": 118.6},
Expand Down Expand Up @@ -203,6 +203,9 @@ def draw(arguments):
PARSER.add_argument('-f', '--force', required=False, default=False,
help="Overwrite output files if they exist already",
action="store_true")
PARSER.add_argument('-ofmt', '--oformat', required=False, default='png',
help="Output format for conversion (pdf requires rsvg-convert)",
metavar='[png/pdf]')
PARSER.add_argument('-v', '--verbose', required=False, default=False,
help="Display verbose output",
action="store_true")
Expand All @@ -214,9 +217,21 @@ def draw(arguments):
if ARGS.build not in ['hg37', 'hg38']:
print(f"\033[91mBuild must be either 'hg37' or 'hg38', you supplied {ARGS.build}.\033[0m")
sys.exit()
if shutil.which("rsvg", mode=os.X_OK) is None:
print(f"\033[91mCould not find `rsvg` in PATH.\033[0m")
sys.exit()

if shutil.which("rsvg-convert", mode=os.X_OK) is None:
if shutil.which("rsvg", mode=os.X_OK) is None:
print(f"\033[91mCould not find `rsvg` or `rsvg-convert` in PATH.\033[0m")
sys.exit()
else:
RSVG = True
if ARGS.oformat != "png":
print(f"\033[93m`rsvg` only supports PNG output, using png\033[0m")
ARGS.oformat = "png"
else:
RSVG = False
if ARGS.oformat not in ["png", "pdf"]:
print(f"\033[93m{ARGS.oformat} is not PNG or PDF, using PNG\033[0m")
ARGS.oformat = "png"
BASE_PATH = os.path.join(sys.prefix, 'lib', 'tagore-data', 'base.svg.p')
try:
BASE = open(BASE_PATH, 'rb')
Expand All @@ -236,11 +251,17 @@ def draw(arguments):
else:
printif(f"\033[94mSaving to: {ARGS.prefix}.svg\033[0m", ARGS.verbose)
draw(ARGS)
printif(f"\033[94mConverting {ARGS.prefix}.svg -> {ARGS.prefix}.png\033[0m", ARGS.verbose)
printif(f"\033[94mConverting {ARGS.prefix}.svg -> {ARGS.prefix}.{ARGS.oformat} \033[0m",
ARGS.verbose)
try:
subprocess.check_output(f"rsvg {ARGS.prefix}.svg {ARGS.prefix}.png", shell=True)
if RSVG:
subprocess.check_output(f"rsvg {ARGS.prefix}.svg {ARGS.prefix}.{ARGS.oformat} ",
shell=True)
else:
subprocess.check_output(f"rsvg-convert -o {ARGS.prefix}.{ARGS.oformat} -f {ARGS.oformat} {ARGS.prefix}.svg ", shell=True)
except subprocess.CalledProcessError as rsvg_e:
printif(f"\033[91mFailed SVG to PNG conversion...\033[0m", ARGS.verbose)
raise rsvg_e
finally:
printif(f"\033[92mSuccessfully converted SVG to PNG\033[0m", ARGS.verbose)
printif(f"\033[92mSuccessfully converted SVG to {ARGS.oformat.upper()}\033[0m",
ARGS.verbose)

0 comments on commit c5d0016

Please sign in to comment.