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yarden / MISO

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
http://genes.mit.edu/burgelab/miso/index.html
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IndexError when summarizing and comparing MISO results #98

Closed althornt closed 7 years ago

althornt commented 7 years ago

I was able to run MISO without errors but I get the following error when trying to summarize or compare the results.

when trying to run the following command: summarize_miso --summarize-samples 15_cfz_AMO1_4_S6 summary_15_cfz_AMO1_4_S6

I get the error: Traceback (most recent call last): File "/pod/home/althornt/miso/miso/bin/compare_miso", line 9, in load_entry_point('misopy==0.5.3', 'console_scripts', 'compare_miso')() File "/pod/home/althornt/miso/miso/lib/python2.7/site-packages/misopy/compare_miso.py", line 94, in main use_compressed=use_compressed) File "/pod/home/althornt/miso/miso/lib/python2.7/site-packages/misopy/hypothesis_test.py", line 289, in output_samples_comparison confidence_level=alpha) File "/pod/home/althornt/miso/miso/lib/python2.7/site-packages/misopy/credible_intervals.py", line 22, in format_credible_intervals cred_interval = compute_credible_intervals(samples) File "/pod/home/althornt/miso/miso/lib/python2.7/site-packages/misopy/credible_intervals.py", line 54, in compute_credible_intervals cred_interval = [samples[lower_bound_indx], samples[upper_bound_indx]] IndexError: only integers, slices (:), ellipsis (...), numpy.newaxis (None) and integer or boolean arrays are valid indices

Any help would be greatly appreciated!

KatyBrown commented 7 years ago

Hi - I also have this problem when running summarize_miso and compare_miso. Thanks!

maofengbiao commented 7 years ago

Hi, I also have this problem. But how to solve it?

maofengbiao commented 7 years ago

Who know the email address of the author?

KatyBrown commented 7 years ago

I have "fixed" it in my local copy by altering credible_intervals.py - changing 

lower_bound_indx = round((alpha/2)*num_samples) - 1
upper_bound_indx = round((1-alpha/2)*num_samples) - 1

to

lower_bound_indx = int(round((alpha/2)*num_samples) - 1)
upper_bound_indx = int(round((1-alpha/2)*num_samples) - 1)

The code now runs, however I can't totally understand what this section does so I don't know if this workaround will have unwanted effects.

althornt commented 7 years ago

Thanks for the fix, Katy!

maofengbiao commented 7 years ago

Thanks a lot.

2017-04-17 0:05 GMT-04:00 Alexis notifications@github.com:

Thanks for the fix, Katy!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/yarden/MISO/issues/98#issuecomment-294401194, or mute the thread https://github.com/notifications/unsubscribe-auth/AGAQpEDpWiISbDh6C5D5-Nw8Tao8toM6ks5rwuUBgaJpZM4Mr8zE .

brightchan commented 7 years ago

Having the same problem and solved with Katy's method, although don't know if it's right to do so. Thanks!

biobenkj commented 7 years ago

Also referenced in #103 as a fix and per @roryk it is now incorporated as a fix.