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

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

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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