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 <[email protected]> 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 > > > > *ANIL KESARWANI, PhD* > Postdoctoral Associate > in Bioinformatics > > Yale Cancer Center > , Section of Hematology > > 300 George Street > , > Suite 787, New Haven CT 06510 USA > Email: > [email protected] <[email protected]> Office : +1 203 737 > 6990 Fax: 203 785 7232 <(203)%20785-7232> > LinkedIn: > https://www.linkedin.com/in/anil-kesarwani-4081889 > <[email protected]> > > _______________________________________________ > miso-users mailing list > [email protected] > http://mailman.mit.edu/mailman/listinfo/miso-users > > -- Erin Wissink, PhD Postdoctoral Fellow, UCLA
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