<html><head><style type='text/css'>p { margin: 0; }</style></head><body><div style='font-family: arial,helvetica,sans-serif; font-size: 12pt; color: #000000'><font face="arial, helvetica, sans-serif" size="3">Hi Yarden,</font><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br>Thanks for the quick reply. The version of misopy that is installed is 0.4.9. I'm explicitly calling the python 2.7 executable when I run these scripts:</div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><div>$ /share/apps/bin/python2.7 -V</div><div>Python 2.7.2</div></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;">Perhaps one of the scripts that is being executed is calling the python in my path (2.4.3)? If I grep for 'python' on all of the .py files in the package, I can see a few lines where it seems to be calling the python in the user's path. For example, the run_events_analysis.py contains the following line:</div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br></div><div><font face="arial, helvetica, sans-serif">"python %s --compute-genes-from-file \"%s\" %s %s --read-len %d "</font></div><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">If I prepend my PATH with the path to the python that miso should be using, the test seem to run just fine. I suppose I can have users add the proper version of python to their path, but this seems like a bug that should be fixed.</font></div><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">Thanks,</font></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;"><br></div><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; font-size: 12pt;">J<br><br><div><span name="x"></span><div style="color: rgb(0, 0, 0); font-family: arial, helvetica, sans-serif; "><div><span style="font-family: arial, helvetica, sans-serif; font-size: 12pt; "><br></span></div><div><span style="font-family: arial, helvetica, sans-serif; font-size: 12pt; ">--</span></div></div><font class="Apple-style-span" face="garamond, 'new york', times, serif" style="font-family: arial, helvetica, sans-serif; color: rgb(0, 0, 0); "><b>Jason Greenbaum, Ph.D.<br></b>Manager, Bioinformatics Core | <a href="mailto:jgbaum@liai.org">jgbaum@liai.org</a><br>La Jolla Institute for Allergy and Immunology</font><div><font class="Apple-style-span" face="garamond, 'new york', times, serif" style="font-family: arial, helvetica, sans-serif; color: rgb(0, 0, 0); "><br></font></div><div><font class="Apple-style-span" face="garamond, 'new york', times, serif" style="font-family: arial, helvetica, sans-serif; color: rgb(0, 0, 0); "><br></font></div><span name="x"></span><br></div><hr id="zwchr"><blockquote style="border-left:2px solid #1010FF;margin-left:5px;padding-left:5px;color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;"><b>From: </b>"Yarden Katz" <yarden@mit.edu><br><b>To: </b>"J. Greenbaum" <jgbaum@liai.org><br><b>Cc: </b>miso-users@mit.edu, "Lukas Chavez Wurm" <lchavez@liai.org><br><b>Sent: </b>Wednesday, July 17, 2013 3:15:51 PM<br><b>Subject: </b>Re: [miso-users] MISO tests appear to be failing<br><br>Hi,<br><br>Could you please let me know which MISO version you are using? Is it 0.4.9?<br><br>One cause of this error this is a mixup between an old and a new version of Python. Older versions of Python do not support the syntax "with open(...)" and that might cause that. Although you're intending to use Python 2.7 which definitely is recent enough to support this, note that the tests call:<br><br>> python /share/apps/lib/python2.7/site-packages/misopy/index_gff.py ...<br><br>which means that whatever Python is available in your environment will be invoked, and if that one is significantly older, it could cause the issue.<br><br>Could you please let me know what the output of these commands is?<br><br>$ /usr/bin/env python -v <br>$ python -v<br><br>Thanks. Best, --Yarden<br><br><br><br>On Jul 17, 2013, at 5:58 PM, J. Greenbaum wrote:<br><br>> Hi all,<br>> <br>> I've recently installed MISO (and all prerequisites) on our cluster and have run into an issue when I run the test_miso.py script (output below). I was hoping someone might have had a similar experience but haven't had any luck searching the archives for these error messages. I've posted the output of test_miso.py and module_availability.py as well as the versions of each of the prerequisite modules below. Any insight would be appreciated. If more information is required, please let me know.<br>> <br>> Thanks in advance,<br>> <br>> J<br>> <br>> <br>> Output of test_miso.py:<br>> [jgbaum@compute-0-6 site-packages]$ /share/apps/bin/python2.7 misopy/test_miso.py <br>> Testing fr-unstranded...<br>> Checking read f_read against +<br>> Checking read f_read against -<br>> Checking read r_read against +<br>> Checking read r_read against -<br>> Testing fr-firststrand...<br>> Testing fr-secondstrand...<br>> .Testing conversion of SAM to BAM...<br>> Executing: python /share/apps/lib/python2.7/site-packages/misopy/sam_to_bam.py --convert /share/apps/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output<br>> Converting SAM to BAM...<br>> - Executing: samtools view -Sbh /share/apps/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam > /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.bam<br>> [samopen] SAM header is present: 35 sequences.<br>> Sorting BAM file...<br>> - Executing: samtools sort /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.bam /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted<br>> Indexing BAM...<br>> - Executing: samtools index /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam<br>> Conversion took 0.00 minutes.<br>> .Testing gene-level Psi...<br>> Testing GFF indexing of: /share/apps/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff<br>> Executing: python /share/apps/lib/python2.7/site-packages/misopy/index_gff.py --index /share/apps/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /share/apps/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed<br>> File "/share/apps/lib/python2.7/site-packages/misopy/index_gff.py", line 151<br>> with open(gff_filename) as gff_in:<br>> ^<br>> SyntaxError: invalid syntax<br>> Executing: python /share/apps/lib/python2.7/site-packages/misopy/run_events_analysis.py --compute-genes-psi /share/apps/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /share/apps/lib/python2.7/site-packages/misopy/test-output/gene-psi-output --read-len 35 <br>> File "/share/apps/lib/python2.7/site-packages/misopy/run_events_analysis.py", line 123<br>> with open(batch_fname, "w") as batch_out:<br>> ^<br>> SyntaxError: invalid syntax<br>> .<br>> ----------------------------------------------------------------------<br>> Ran 3 tests in 0.177s<br>> <br>> OK<br>> <br>> <br>> Output of module_availability.py:<br>> [jgbaum@compute-0-6 site-packages]$ /share/apps/bin/python2.7 misopy/module_availability.py<br>> Looking for required Python modules..<br>> Checking for availability of: numpy<br>> Checking for availability of: scipy<br>> Checking for availability of: json<br>> Checking for availability of: matplotlib<br>> Checking for availability of: pysam<br>> All modules are available!<br>> Looking for required executables..<br>> Checking if samtools is available<br>> - samtools is available<br>> Checking if bedtools is available<br>> - bedtools is available<br>> <br>> <br>> Module/program versions:<br>> pysam 0.7.4<br>> numpy 1.6.1<br>> scipy 0.9.0<br>> matplotlib: 1.1.0<br>> samtools: 0.1.18<br>> bedtools: v2.16.2-zip-466a9f0<br>> Python: 2.7<br>> <br>> <br>> --<br>> Jason Greenbaum, Ph.D.<br>> Manager, Bioinformatics Core | jgbaum@liai.org<br>> La Jolla Institute for Allergy and Immunology<br>> <br>> <br>> <br>> _______________________________________________<br>> miso-users mailing list<br>> miso-users@mit.edu<br>> http://mailman.mit.edu/mailman/listinfo/miso-users<br><br></blockquote><br></div></div></body></html>