<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif;" dir="ltr">
<div id="divtagdefaultwrapper" style="font-size: 12pt; color: rgb(0, 0, 0); font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols;" dir="ltr">
<p style="margin-top:0;margin-bottom:0">Hello,</p>
<p style="margin-top:0;margin-bottom:0">I think there is a major issue with sashimi_plot version vs miso version.</p>
<p style="margin-top:0;margin-bottom:0">TL;DR: <b>sashimi_plot need ".miso" files, which are removed by "miso_pack" function since Miso 0.5.0.</b></p>
<p style="margin-top:0;margin-bottom:0"><span style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">In fact m</span><span style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">iso_pack
will pick up all the .miso files under each chr* folder and put them into a .miso_db </span><span style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;"></span><span style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">file</span><span style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">,
and remove those .miso files.</span><br>
</p>
<p style="margin-top:0;margin-bottom:0"><b>Temporary solution: Make a copy of ".miso" files right after miso --run.</b><span style="font-size: 12pt;"> According to the manual miso_zip will also pack the files if that's not done already. </span></p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"></p>
<p style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">
<span style="font-size: 12pt;">Now to answer Jermaine Jenkins:</span><br>
</p>
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 12pt;"> </span></p>
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 12pt;">You are probably using a different version of Miso, and the t</span><span style="font-size: 12pt;">est files are partially missing and / or files structure is not correct.</span></p>
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 12pt;"><br>
</span></p>
<p style="margin-top:0;margin-bottom:0">In my legace files of miso 0.4.9, the test-data/miso-data contains folders </p>
<p style="margin-top:0;margin-bottom:0"><span>"heartWT1", "heartWT2", "heartKOa", "heartKOb" </span><br>
</p>
<p style="margin-top:0;margin-bottom:0"><span>and under each of those folders there is a file named "<span>chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso"</span><span></span></span></p>
<p style="margin-top:0;margin-bottom:0"><span><span><br>
</span></span></p>
<p style="margin-top:0;margin-bottom:0"><span><span>When I run my current miso/sashimi package (miso 0.5.3) on those test data, everything is OK and I got my output as in the manual.</span></span></p>
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 12pt;">>From the setting files, and from the flow of the analysis, I would assume that you need 4 bam files (one for each sample) and 4 miso output folders. Thus you need 4 .miso files for the test.
Except in my 0.5.3 test files I have just one .miso file</span><span style="font-size: 12pt;"> under /miso-data . When I do the test on that set of test data, I got the sashimi plot without BF intervals on the right of the output.</span><br>
</p>
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 12pt;"><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span><span><br>
</span></span></p>
<p style="margin-top:0;margin-bottom:0"><span><span><br>
</span></span></p>
<p style="margin-top:0;margin-bottom:0"><span><span><b>Questions to developpers:</b></span></span></p>
<p style="margin-top:0;margin-bottom:0"><span><span><br>
</span></span></p>
<p style="margin-top:0;margin-bottom:0"><span><span>When I tried to download from the git <a href="https://github.com/yarden/MISO/zipball/fastmiso" class="OWAAutoLink">https://github.com/yarden/MISO/zipball/fastmiso</a> it seems to point to miso0.4.9 (file
name <span>yarden-MISO-1ca049f).</span></span></span></p>
<p style="margin-top:0;margin-bottom:0">Can you confirm that pip / last commit on git / zip download all point to the same version?</p>
<p style="margin-top:0;margin-bottom:0"><b>Is there a more recent version of sashimi plot that no longer relies on .miso files but on .miso_db files?
</b>On the current git the test files still contain .miso files, so I wonder if sashimi plot is ever updated since Miso 0.5.0. In fact, t<span style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">he
miso_pack is released within Miso 0.5.0 during Feb 20, 2014, while the last sashimi_plot update was in Feb 11 2014.</span><span style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;"> On
the git, the last commit on sashimi_plot is Feb 23 2014 while the last commit on Miso is Aug 2017 in the same time of Miso 0.5.4. </span></p>
<p style="margin-top:0;margin-bottom:0"><span><span><br>
</span></span></p>
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 12pt;">Delong</span><br>
</p>
<p style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">
<br>
</p>
<p style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">
<br>
</p>
<p style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">
<br>
</p>
<p style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">
</p>
<p style="font-family: Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">
<br>
</p>
<br>
<p></p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> miso-users-bounces@mit.edu <miso-users-bounces@mit.edu> on behalf of Jermaine Jenkins <jljbbc88@gmail.com><br>
<b>Sent:</b> April 9, 2018 7:58:08 PM<br>
<b>To:</b> miso-users@mit.edu<br>
<b>Subject:</b> [miso-users] error in testing sashimi_plot</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div>
<div>
<div>Hi,<br>
<br>
</div>
Whe trying to test sashimi_plot I am getting a errors and a plot without MISO estimates? Any help is appreciated.<br>
<br>
</div>
Thanks,<br>
</div>
JJ<br>
<div>
<div><br>
</div>
<div>part of the terminal output (full output is attached)<br>
</div>
<div>
<div><br>
miso_prefix: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data<br>
Searching for MISO files in: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT1<br>
- Looking for chromosome chr17 directories<br>
Error: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT1 not a directory.<br>
Error: Could not find MISO output files for sample heartWT1 (after searching in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT1 and its subdirectories). Are you sure MISO
output files are present in that directory?<br>
Searching for MISO files in: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT2<br>
- Looking for chromosome chr17 directories<br>
Error: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT2 not a directory.<br>
Error: Could not find MISO output files for sample heartWT2 (after searching in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT2 and its subdirectories). Are you sure MISO
output files are present in that directory?<br>
Searching for MISO files in: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOa<br>
- Looking for chromosome chr17 directories<br>
Error: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOa not a directory.<br>
Error: Could not find MISO output files for sample heartKOa (after searching in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOa and its subdirectories). Are you sure MISO
output files are present in that directory?<br>
Searching for MISO files in: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOb<br>
- Looking for chromosome chr17 directories<br>
Error: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOb not a directory.<br>
Error: Could not find MISO output files for sample heartKOb (after searching in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOb and its subdirectories). Are you sure MISO
output files are present in that directory?<br>
Reading dimensions from settings...<br>
- Height: 5.00<br>
- Width: 7.00<br>
Plotting read densities and MISO estimates along event...<br>
- Event: chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-<br>
Setting up plot using dimensions: [7.0, 5.0]<br>
Using intron scale 30.0<br>
Using exon scale 4.0<br>
Reading sample label: heartWT1.sorted.bam<br>
Processing BAM: ./test-data/bam-data/heartWT1.sorted.bam<br>
Warning: MISO file not found<br>
Loading MISO file: <br>
Posterior plot failed.<br>
Reading sample label: heartWT2.sorted.bam<br>
Processing BAM: ./test-data/bam-data/heartWT2.sorted.bam<br>
Warning: MISO file not found<br>
Loading MISO file: <br>
Posterior plot failed.<br>
Reading sample label: heartKOa.sorted.bam<br>
Processing BAM: ./test-data/bam-data/heartKOa.sorted.bam<br>
Warning: MISO file not found<br>
Loading MISO file: <br>
Posterior plot failed.<br>
Reading sample label: heartKOb.sorted.bam<br>
Processing BAM: ./test-data/bam-data/heartKOb.sorted.bam<br>
Warning: MISO file not found<br>
Loading MISO file: <br>
Posterior plot failed.<br>
Saving plot to: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-plot/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.pdf<br>
</div>
</div>
</div>
</div>
</div>
</div>
</body>
</html>