[miso-users] question about compare_miso

[Ou, Jianhong]

Hi all,

I am running miso (0.5.2). I downloaded annotation file from  http://genes.mit.edu/burgelab/miso/annotations/miso_annotations_hg19_v1.zip, and unzipped the files, Then I run

unzip miso_annotations_hg19_v1.zip

for gff in A3SS A5SS SE ALE MXE RI TandemUTR
do
   index_gff --index $gff.hg19.gff3 indexed_${gff}_events/
done

for gff in SE A3SS A5SS ALE MXE RI TandemUTR
do
      miso --run /home/jo83w/miso/hg19/indexed_${gff}_events/ ${bams[$i]} --output-dir ${tag[$i]}.${gff}/ --read-len 100 -p 16 --paired-end 165 50 --event-type ${gff}
      summarize_miso --summarize-samples ${tag[$i]}.${gff}/ ${tag[$i]}.${gff}.summaries/
done

for gff in SE A3SS A5SS ALE MXE RI TandemUTR
do
compare_miso --compare-samples NS.${gff}/ ${tag[$i]}.${gff}/ ${tag[$i]}.${gff}.comparison/
done

Until compare_miso, everything goes smoothly. However, I got error when run compare_miso,

$ compare_miso --compare-samples FOX.MXE/ NS.MXE/ FOX.MXE.comparison/
Given output dir: /project/miso/FOX.MXE.comparison
Retrieving MISO files in sample directories...
Computing sample comparison between /project/miso/FOX.MXE and /project/miso/NS.MXE...
  - No. of events in /project/miso/FOX.MXE: 2322
  - No. of events in /project/miso/NS.MXE: 2241
Creating comparisons parent directory: /project/miso/FOX.MXE.comparison/FOX.MXE_vs_NS.MXE
WARNING: Could not parse event chr18:30661555:30661638:+ at chr18:30663362:30663451:+ at chr18:30672056:30672133:+ at chr18:30682258:30682345:+ samples
WARNING: Could not parse event chr19:42517388:42517999:+ at chr19:42527352:42527516:+ at chr19:42527676:42527763:+ at chr19:42529932:42530058:+ samples
Traceback (most recent call last):
  File "/share/pkg/python/2.7.5/bin/compare_miso", line 9, in <module>
    load_entry_point('misopy==0.5.2', 'console_scripts', 'compare_miso')()
  File "/share/pkg/python/2.7.5/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/compare_miso.py", line 94, in main
    use_compressed=use_compressed)
  File "/share/pkg/python/2.7.5/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/hypothesis_test.py", line 274, in output_samples_comparison
    sample2_label=sample2_label)
  File "/share/pkg/python/2.7.5/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/hypothesis_test.py", line 148, in compute_delta_densities
    posterior_samples2[:, iso_num]
IndexError: too many indices

$ compare_miso --compare-samples NS.MXE/ FOX.MXE/ FOX.MXE.comparison/
Given output dir: /project/miso/FOX.MXE.comparison
Retrieving MISO files in sample directories...
Computing sample comparison between /project/miso/NS.MXE and /project/umw_pgfe_michael_green/iCLIP/18APR14_PE100_C4AK4AC-B/miso/FOX.MXE...
  - No. of events in /project/miso/NS.MXE: 2241
  - No. of events in /project/miso/FOX.MXE: 2322
Creating comparisons parent directory: /project/FOX.MXE.comparison/NS.MXE_vs_FOX.MXE
WARNING: Could not parse event chr18:30661555:30661638:+ at chr18:30663362:30663451:+ at chr18:30672056:30672133:+ at chr18:30682258:30682345:+ samples
Traceback (most recent call last):
  File "/share/pkg/python/2.7.5/bin/compare_miso", line 9, in <module>
    load_entry_point('misopy==0.5.2', 'console_scripts', 'compare_miso')()
  File "/share/pkg/python/2.7.5/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/compare_miso.py", line 94, in main
    use_compressed=use_compressed)
  File "/share/pkg/python/2.7.5/lib/python2.7/site-packages/misopy-0.5.2-py2.7-linux-x86_64.egg/misopy/hypothesis_test.py", line 255, in output_samples_comparison
    samples1 = sample1_results[0]
TypeError: 'NoneType' object has no attribute '__getitem__'

Could anybody help me to figure out this error? Thank you very much.

Yours Sincerely,

Jianhong Ou

LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
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