[miso-users] AttributeError when testing MISO-Sashimi plot

[Yarden Katz]

Hi Sandy,

It sounds like you might be using an older version of pysam.  The "positions" attribute was added around pysam 0.5.  See: 

http://www.cgat.org/~andreas/documentation/pysam/release.html#release-0-6

I recommend installing the latest pysam (0.6) and using that. 

Best, --Yarden

On Mar 12, 2012, at 3:07 AM, ·½Ïþæà wrote:

> Dear Yarden,
> 
> Hi~!
> I've built misopy-0.4.1 in the linux os via location "~/tmp/misopy/",
> and I would like to test the sashimi-plot, then I encounter one error saying " AttributeError: 'csamtools.AlignedRead' object has no attribute 'positions' ".
> Hope you can check the warning messages and help me out! thx!
> 
> the detail warning messages are below:
> ===========================================
> ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot$ python ./plot.py --plot-event "chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-" test-data/event-data/ settings/sashimi_plot_settings.txt --output-dir test-plot
> 
> /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: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data
> Searching for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartWT1
>   - Looking for chromosome chr17 directories
> Looking for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartWT1/chr17
> Found chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:- MISO file.
>   - Location: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartWT1/chr17/chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.miso
> Searching for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartWT2
>   - Looking for chromosome chr17 directories
> Looking for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartWT2/chr17
> Found chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:- MISO file.
>   - Location: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartWT2/chr17/chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.miso
> Searching for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartKOa
>   - Looking for chromosome chr17 directories
> Looking for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartKOa/chr17
> Found chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:- MISO file.
>   - Location: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartKOa/chr17/chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.miso
> Searching for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartKOb
>   - Looking for chromosome chr17 directories
> Looking for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartKOb/chr17
> Found chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:- MISO file.
>   - Location: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartKOb/chr17/chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.miso
> Plotting read densities and MISO estimates along event...
>   - Event: chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-
> miso_prefix: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data
> Searching for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartWT1
>   - Looking for chromosome chr17 directories
> Looking for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartWT1/chr17
> Found chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:- MISO file.
>   - Location: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartWT1/chr17/chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.miso
> Searching for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartWT2
>   - Looking for chromosome chr17 directories
> Looking for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartWT2/chr17
> Found chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:- MISO file.
>   - Location: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartWT2/chr17/chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.miso
> Searching for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartKOa
>   - Looking for chromosome chr17 directories
> Looking for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartKOa/chr17
> Found chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:- MISO file.
>   - Location: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartKOa/chr17/chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.miso
> Searching for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartKOb
>   - Looking for chromosome chr17 directories
> Looking for MISO files in: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartKOb/chr17
> Found chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:- MISO file.
>   - Location: ~/tmp/misopy/misopy-0.4.1/misopy/sashimi_plot/test-data/miso-data/heartKOb/chr17/chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.miso
> Loading BAM filename from: ./test-data/bam-data/heartWT1.sorted.bam
> Loading took 0.00 seconds
> 
> Traceback (most recent call last):
>   File "./plot.py", line 282, in <module>
>     main()
>   File "./plot.py", line 278, in main
>     plot_event(event_name, pickle_dir, settings_filename, output_dir)
>   File "./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 35, in plot_density_single
>     wiggle, jxns =readsToWiggle_pysam(subset_reads,tx_start, tx_end)
>   File "/usr/local/lib/python2.6/dist-packages/misopy/sashimi_plot/plot_utils/plot_gene.py", line 286, in readsToWiggle_pysam
>     aligned_positions = read.positions
> AttributeError: 'csamtools.AlignedRead' object has no attribute 'positions'
> ==================================================
> 
> Thanks all so much & best
> 
> Sandy FANG
> 
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