[miso-users] sashimi plot error

[Renaud Desgraz]

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_re
sources.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_re
sources.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.eg
g/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.eg
g/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.eg
g/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.eg
g/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.eg
g/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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