<div dir="ltr">Hi Anil (and rest of MISO),<div><br></div><div>I had this problem and fixed it pretty easily. I edited the file credible_intervals.py in two places:</div><div><br></div><div><div style="font-size:12.8px">line 47: lower_bound_indx = int(round((alpha/2)*num_<wbr>samples) - 1)</div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">line 50: upper_bound_indx = int(round((1-alpha/2)*num_<wbr>samples) - 1)</div></div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">Erin</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Mar 25, 2017 at 12:08 PM, Anil Kesarwani <span dir="ltr"><<a href="mailto:kesarwani.anil@gmail.com" target="_blank">kesarwani.anil@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Dear MISO Developer,<br><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">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.<br><br>STEP1<br>miso --run $SE $Control_1a --output-dir $outdir/$name/control --read-len 101 --paired-end 250 15 --settings-filename $setting_file <br>STEP2<br>miso_pack --pack $outdir/$name/control <br>STEP3<br>summarize_miso --summarize-samples $outdir/$name/srsf4 $outdir/$name/srsf4 <br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>Loading events from: /projects/kesara/SR/MISO/SE/<wbr>srsf4<br>Writing summary to: /projects/kesara/SR/MISO/SE/<wbr>srsf4/summary/srsf4.miso_<wbr>summary<br>Traceback (most recent call last):<br> File "/opt/compsci/python/2.7.3/<wbr>bin/summarize_miso", line 9, in <module><br> load_entry_point('misopy==0.5.<wbr>3', 'console_scripts', 'summarize_miso')()<br> File "/opt/compsci/python/2.7.3/<wbr>lib/python2.7/site-packages/<wbr>misopy/summarize_miso.py", line 93, in main<br> use_compressed=use_compressed)<br> File "/opt/compsci/python/2.7.3/<wbr>lib/python2.7/site-packages/<wbr>misopy/samples_utils.py", line 309, in summarize_sampler_results<br> output_fields = format_credible_intervals(<wbr>event_name, samples)<br> File "/opt/compsci/python/2.7.3/<wbr>lib/python2.7/site-packages/<wbr>misopy/credible_intervals.py", line 22, in format_credible_intervals<br> cred_interval = compute_credible_intervals(<wbr>samples)<br> File "/opt/compsci/python/2.7.3/<wbr>lib/python2.7/site-packages/<wbr>misopy/credible_intervals.py", line 54, in compute_credible_intervals<br> cred_interval = [samples[lower_bound_indx], samples[upper_bound_indx]]<br>IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices<br clear="all"></div><div><div class="m_3071004397533321830gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><span style="color:rgb(0,0,0)"><span style="font-family:arial,helvetica,sans-serif"><b><br><br><br>A<div style="display:inline">NIL KESARWANI</div>, PhD</b><br></span></span></div><div><span style="color:rgb(0,0,0)"><span style="font-family:arial,helvetica,sans-serif">Postdoctoral Associate<div style="display:inline"> in Bioinformatics</div><br></span></span></div><div><span style="color:rgb(0,0,0)"><span style="font-family:arial,helvetica,sans-serif"><font size="2">Yale Cancer Center<div style="display:inline">, Section of Hematology</div><br></font></span></span></div><div><span style="color:rgb(0,0,0)"><span style="font-family:arial,helvetica,sans-serif">300 George Street<div style="display:inline">,</div> Suite 787, New Haven CT 06510 USA</span></span></div><div><span style="color:rgb(0,0,0)"><span style="font-family:arial,helvetica,sans-serif"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice">Email: </span></span></span></span></span></span></span><span style="font-family:arial,helvetica,sans-serif"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><div style="display:inline"><a href="mailto:nil.kesarwani@yale.edu" target="_blank">kesarwani.anil@gmail.com</a> <span><span style="font-family:arial,helvetica,sans-serif"><font size="2">Office : <span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><a href="tel:%2B1%20203%20737%206990" value="+12037376990" target="_blank">+1 203 737 6990</a> Fax: <a href="tel:(203)%20785-7232" value="+12037857232" target="_blank">203 785 7232</a></span></span></span></span></span></font></span></span></div></span></span></span></span></span></span></span></span></div><div><span style="font-family:arial,helvetica,sans-serif"><font size="2"><span style="color:rgb(0,0,0)"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><span title="Call with Google Voice"><div style="display:inline">LinkedIn: </div></span></span></span></span></span></span></span><span style="color:rgb(0,0,0)"><a href="https://www.linkedin.com/in/anil-kesarwani-4081889" target="_blank">https://www.linkedin.com/in/<wbr>anil-kesarwani-4081889</a></span><a href="mailto:Kesarwani.anil@gmail.com" target="_blank"></a></font></span></div></div></div></div></div></div></div></div></div></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Erin Wissink, PhD<div>Postdoctoral Fellow, UCLA</div></div></div>
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