[miso-users] Error during summarize_miso

[Erin Wissink]

Hi Anil (and rest of MISO),

I had this problem and fixed it pretty easily. I edited the file
credible_intervals.py in two places:

line 47: lower_bound_indx = int(round((alpha/2)*num_samples) - 1)

line 50: upper_bound_indx = int(round((1-alpha/2)*num_samples) - 1)

Erin

On Sat, Mar 25, 2017 at 12:08 PM, Anil Kesarwani <kesarwani.anil at gmail.com>
wrote:

> Dear MISO Developer,
>
> I ran the three steps of MISO, but the error during third step. Could you
> please take a look and resolve the issue. Your response is highly
> appreciated.
>
> STEP1
> miso --run $SE $Control_1a --output-dir $outdir/$name/control --read-len
> 101 --paired-end 250 15 --settings-filename $setting_file
> STEP2
> miso_pack --pack $outdir/$name/control
> STEP3
> summarize_miso --summarize-samples $outdir/$name/srsf4 $outdir/$name/srsf4
>
> Loading events from: /projects/kesara/SR/MISO/SE/srsf4
> Writing summary to: /projects/kesara/SR/MISO/SE/srsf4/summary/srsf4.miso_
> summary
> Traceback (most recent call last):
>   File "/opt/compsci/python/2.7.3/bin/summarize_miso", line 9, in <module>
>     load_entry_point('misopy==0.5.3', 'console_scripts',
> 'summarize_miso')()
>   File "/opt/compsci/python/2.7.3/lib/python2.7/site-packages/misopy/summarize_miso.py",
> line 93, in main
>     use_compressed=use_compressed)
>   File "/opt/compsci/python/2.7.3/lib/python2.7/site-packages/misopy/samples_utils.py",
> line 309, in summarize_sampler_results
>     output_fields = format_credible_intervals(event_name, samples)
>   File "/opt/compsci/python/2.7.3/lib/python2.7/site-packages/misopy/credible_intervals.py",
> line 22, in format_credible_intervals
>     cred_interval = compute_credible_intervals(samples)
>   File "/opt/compsci/python/2.7.3/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
>
>
>
> *A​NIL KESARWANI, PhD*
> Postdoctoral Associate
> ​ in Bioinformatics​
>
> Yale Cancer Center
> ​, Section of Hema​tology
>
> 300 George Street
> ​,​
> Suite 787, New Haven CT 06510 USA
> Email:
> kesarwani.anil at gmail.com <nil.kesarwani at yale.edu>  Office : +1 203 737
> 6990 Fax: 203 785 7232 <(203)%20785-7232>
> LinkedIn​:
> https://www.linkedin.com/in/anil-kesarwani-4081889​
> <Kesarwani.anil at gmail.com>
>
> _______________________________________________
> miso-users mailing list
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>
>


-- 
Erin Wissink, PhD
Postdoctoral Fellow, UCLA
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