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tanghaibao / jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics
BSD 2-Clause "Simplified" License
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output format of jcvi.graphics.karyotype #296

Closed qymeng1996 closed 4 years ago

qymeng1996 commented 4 years ago

Dear Professor Haibao Tang, I can get the PDF format file by use "python -m jcvi.graphics.karyotype seqids layout", however when I modify the format, I met an error: python -m jcvi.graphics.karyotype --format=emf --figsize=14x7 seqids layout 09:54:13 [base] Load file layout 09:54:13 [base] Load file bgi.bed 09:54:15 [base] Load file nbi.bed 09:54:18 [base] savefig failed. Reset usetex to False. Format 'emf' is not supported (supported formats: eps, jpeg, jpg, pdf, pgf, png, ps, raw, rgba, svg, svgz, tif, tiff) Traceback (most recent call last): File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/site-packages/jcvi/graphics/base.py", line 269, in savefig plt.savefig(figname, dpi=dpi, format=format) File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/site-packages/matplotlib/pyplot.py", line 722, in savefig res = fig.savefig(*args, kwargs) File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/site-packages/matplotlib/figure.py", line 2180, in savefig self.canvas.print_figure(fname, kwargs) File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 2014, in print_figure canvas = self._get_output_canvas(format) File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 1956, in _get_output_canvas .format(fmt, ", ".join(sorted(self.get_supported_filetypes())))) ValueError: Format 'emf' is not supported (supported formats: eps, jpeg, jpg, pdf, pgf, png, ps, raw, rgba, svg, svgz, tif, tiff)

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/runpy.py", line 193, in _run_module_as_main "main", mod_spec) File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/site-packages/jcvi/graphics/karyotype.py", line 435, in main() File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/site-packages/jcvi/graphics/karyotype.py", line 431, in main savefig(image_name, dpi=iopts.dpi, iopts=iopts) File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/site-packages/jcvi/graphics/base.py", line 275, in savefig plt.savefig(figname, dpi=dpi) File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/site-packages/matplotlib/pyplot.py", line 722, in savefig res = fig.savefig(*args, kwargs) File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/site-packages/matplotlib/figure.py", line 2180, in savefig self.canvas.print_figure(fname, kwargs) File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 2014, in print_figure canvas = self._get_output_canvas(format) File "/home/qymeng/miniconda3/envs/py35/lib/python3.6/site-packages/matplotlib/backend_bases.py", line 1956, in _get_output_canvas .format(fmt, ", ".join(sorted(self.get_supported_filetypes())))) ValueError: Format 'emf' is not supported (supported formats: eps, jpeg, jpg, pdf, pgf, png, ps, raw, rgba, svg, svgz, tif, tiff) Could you give me some advise to solve this error ? Thank you very much.

tanghaibao commented 4 years ago

@qymeng996

It says in the error message:

ValueError: Format 'emf' is not supported (supported formats: eps, jpeg, jpg, pdf, pgf, png, ps, raw, rgba, svg, svgz, tif, tiff)

So use a format within the supported formats.