=?gb2312?B?tPC4tDogW21pc28tdXNlcnNdIEF0dHJpYnV0ZUVycm9yIHdoZW4gdGVzdGlu?= =?gb2312?Q?g_MISO-Sashimi_plot?=

[=?gb2312?B?t73P/ubD?=]

Hi Yarden,

Thank you for your reply, after I updated the pysam 0.6 I now run the test of sashimi-plot sucessfully.
Then I tried plotting 6 events respectively, with one event it kept showing warnings and returns no result, when other 5 were ok.
and it looks like something wrong in module "plot_density_single", yet I am not quite understand, since I used same setting file and input as other 5 events.
Just hope you can check in the below message and give me some more advices, grateful again!!

BTW, it seems that when occurring problems like "AttributeError", I should be sure all the related tools be the newest ones, right?

best

Sandy

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$ python /software/MISO/misopy-0.4.1/misopy/sashimi_plot/plot.py --plot-event "chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+" ~/miso/gff_files/hg19/index/SE/ ~/miso/plot_files/sashimi_plot_settings.txt --output-dir /projects/hsa_colon/miso/plot_files/

/usr/local/lib/python2.6/dist-packages/mpl_toolkits/__init__.py:2: UserWarning: Module dateutil was already imported from /usr/local/lib/python2.6/dist-packages/dateutil/__init__.pyc, but /usr/lib/pymodules/python2.6 is being added to sys.path
  __import__('pkg_resources').declare_namespace(__name__)

miso_prefix:~/miso/output_files/SE

Searching for MISO files in:~/miso/output_files/SE/s1
  - Looking for chromosome chr10 directories
Looking for MISO files in:~/miso/output_files/SE/s1/chr10
Found chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+ MISO file.
  - Location:~/miso/output_files/SE/s1/chr10/chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+.miso

Searching for MISO files in:~/miso/output_files/SE/s2
  - Looking for chromosome chr10 directories
Looking for MISO files in:~/miso/output_files/SE/s2/chr10
Found chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+ MISO file.
  - Location:~/miso/output_files/SE/s2/chr10/chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+.miso

Searching for MISO files in:~/miso/output_files/SE/s3
  - Looking for chromosome chr10 directories
Looking for MISO files in:~/miso/output_files/SE/s3/chr10
Found chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+ MISO file.
  - Location:~/miso/output_files/SE/s3/chr10/chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+.miso

Plotting read densities and MISO estimates along event...
  - Event: chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+
miso_prefix:~/miso/output_files/SE

Searching for MISO files in:~/miso/output_files/SE/s1
  - Looking for chromosome chr10 directories
Looking for MISO files in:~/miso/output_files/SE/s1/chr10
Found chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+ MISO file.
  - Location:~/miso/output_files/SE/s1/chr10/chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+.miso

Searching for MISO files in:~/miso/output_files/SE/s2
  - Looking for chromosome chr10 directories
Looking for MISO files in:~/miso/output_files/SE/s2/chr10
Found chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+ MISO file.
  - Location:~/miso/output_files/SE/s2/chr10/chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+.miso

Searching for MISO files in:~/miso/output_files/SE/s3
  - Looking for chromosome chr10 directories
Looking for MISO files in:~/miso/output_files/SE/s3/chr10
Found chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+ MISO file.
  - Location:~/miso/output_files/SE/s3/chr10/chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+.miso

Loading BAM filename from:~/miso/sam_files/s1/accepted_hits.bam
Loading took 0.00 seconds
Loading MISO file:~/miso/output_files/SE/s1/chr10/chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+.miso
Loading BAM filename from:~/miso/sam_files/s2/accepted_hits.bam
Loading took 0.00 seconds
Loading MISO file:~/miso/output_files/SE/s2/chr10/chr10:111890121:111890244:+ at chr10:111892063:111892158:+ at chr10:111893084:111895452:+.miso
Loading BAM filename from:~/miso/sam_files/s3/accepted_hits.bam
Loading took 0.00 seconds

Traceback (most recent call last):
  File "/software/MISO/misopy-0.4.1/misopy/sashimi_plot/plot.py", line 282, in <module>
    main()
  File "/software/MISO/misopy-0.4.1/misopy/sashimi_plot/plot.py", line 278, in main
    plot_event(event_name, pickle_dir, settings_filename, output_dir)
  File "/software/MISO/misopy-0.4.1/misopy/sashimi_plot/plot.py", line 132, in plot_event
    output_dir)
  File "/usr/local/lib/python2.6/dist-packages/misopy/sashimi_plot/plot_utils/plot_gene.py", line 540, in plot_density_from_file
    plot_density(sashimi_obj, pickle_filename, event)
  File "/usr/local/lib/python2.6/dist-packages/misopy/sashimi_plot/plot_utils/plot_gene.py", line 222, in plot_density
    junction_log_base=junction_log_base)
  File "/usr/local/lib/python2.6/dist-packages/misopy/sashimi_plot/plot_utils/plot_gene.py", line 131, in plot_density_single
    linspace(0, max(graphcoords), nxticks)], fontsize=font_size)
KeyError: 738

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