[miso-users] sashimi plot error

[Yarden Katz]

Hi Renaud,

This error stems from a bug in version 0.4.8 of MISO, which was fixed in 0.4.9 (the latest release).  Upgrading will resolve the problem.

Best, --Yarden



On Jul 30, 2013, at 5:57 PM, Renaud Desgraz wrote:

> Hi,
>  
> I am trying to use sashimi to plot transcript isoforms from my MISO output.
> I am at the Whitehead institute and I am running sashimi on Tak.
>  
> When I enter the following command line:
>  
> plot.py --plot-event ENSMUSG00000090266 /lab/page/frenchie/E14_Dazl_WTvsKO/MISO/GFF_files/indexed/ /lab/page/frenchie/E14_Dazl_WTvsKO/MISO/Sashimi_Plot/sashimi_plot_settings.txt --output-dir ./test-plot/
>  
> I get the following output ending with an error and no plot in my output folder:
>  
> Reading settings from: /lab/page/frenchie/E14_Dazl_WTvsKO/MISO/Sashimi_Plot/sashimi_plot_settings.txt
> Parsing data:bam_prefix
> Parsing data:miso_prefix
> Parsing data:bam_files
> Parsing data:miso_files
> Parsing plotting:fig_width
> Parsing plotting:fig_height
> Parsing plotting:intron_scale
> Parsing plotting:exon_scale
> Parsing plotting:logged
> Parsing plotting:font_size
> Parsing plotting:ymax
> Parsing plotting:show_posteriors
> Parsing plotting:bar_posteriors
> Parsing plotting:number_junctions
> Parsing plotting:resolution
> Parsing plotting:posterior_bins
> Parsing plotting:gene_posterior_ratio
> Parsing plotting:colors
> Parsing plotting:coverages
> Parsing plotting:bar_color
> Parsing plotting:bf_thresholds
> miso_prefix: /lab/page/frenchie/E14_Dazl_WTvsKO/MISO
> Searching for MISO files in: /lab/page/frenchie/E14_Dazl_WTvsKO/MISO/Output_KO
>   - Looking for chromosome chr11 directories
> Looking for MISO files in: /lab/page/frenchie/E14_Dazl_WTvsKO/MISO/Output_KO/chr11
> Found ENSMUSG00000090266 MISO file.
>   - Location: /lab/page/frenchie/E14_Dazl_WTvsKO/MISO/Output_KO/chr11/ENSMUSG00000090266.miso
> Searching for MISO files in: /lab/page/frenchie/E14_Dazl_WTvsKO/MISO/Output_WT
>   - Looking for chromosome chr11 directories
> Looking for MISO files in: /lab/page/frenchie/E14_Dazl_WTvsKO/MISO/Output_WT/chr11
> Found ENSMUSG00000090266 MISO file.
>   - Location: /lab/page/frenchie/E14_Dazl_WTvsKO/MISO/Output_WT/chr11/ENSMUSG00000090266.miso
> Reading dimensions from settings...
> - Height: 5.00
> - Width: 7.00
> Plotting read densities and MISO estimates along event...
>   - Event: ENSMUSG00000090266
> Setting up plot using dimensions:  [7.0, 5.0]
> Using intron scale  30.0
> Using exon scale  4.0
> Traceback (most recent call last):
>   File "/usr/local/bin/plot.py", line 5, in <module>
>     pkg_resources.run_script('misopy==0.4.8', 'plot.py')
>   File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 505, in run_script
>     self.require(requires)[0].run_script(script_name, ns)
>   File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 1245, in run_script
>     execfile(script_filename, namespace, namespace)
>   File "/usr/local/lib/python2.7/dist-packages/misopy-0.4.8-py2.7-linux-x86_64.egg/EGG-INFO/scripts/plot.py", line 341, in <module>
>     main()
>   File "/usr/local/lib/python2.7/dist-packages/misopy-0.4.8-py2.7-linux-x86_64.egg/EGG-INFO/scripts/plot.py", line 335, in main
>     plot_label=plot_label)
>   File "/usr/local/lib/python2.7/dist-packages/misopy-0.4.8-py2.7-linux-x86_64.egg/EGG-INFO/scripts/plot.py", line 154, in plot_event
>     plot_label=plot_label)
>   File "/usr/local/lib/python2.7/dist-packages/misopy-0.4.8-py2.7-linux-x86_64.egg/misopy/sashimi_plot/plot_utils/plot_gene.py", line 683, in plot_density_from_file
>     plot_density(sashimi_obj, pickle_filename, event)
>   File "/usr/local/lib/python2.7/dist-packages/misopy-0.4.8-py2.7-linux-x86_64.egg/misopy/sashimi_plot/plot_utils/plot_gene.py", line 210, in plot_density
>     if plot_title is not None:
> NameError: global name 'plot_title' is not defined
>  
>  
> There must be something I’m doing wrond but I cannot figure out what…?
>  
> Thanks for your help!
>  
>  
> Renaud
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