[miso-users] MISO tests appear to be failing

Wed Jul 17 18:49:08 EDT 2013

Hi,

Yes, as I wrote in the first email the scripts internally call "python" so the Python on your PATH gets invoked.

I don't consider it a bug because I'm not aware of any generic way to get the appropriate Python programmatically (one of the many problems with Python packaging in general).  There's no way for the script to know that you favor Python 2.7 over Python 2.4.3, so the standard Unix convention, which seems reasonable, is for me to invoke "python" and have the user adjust it so that the preferred Python is found first in the PATH environment variable.  

Best, --Yarden

On Jul 17, 2013, at 6:33 PM, J. Greenbaum wrote:

> Hi Yarden,
> 
> 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:
> 
> $ /share/apps/bin/python2.7 -V
> Python 2.7.2
> 
> 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:
> 
> "python %s --compute-genes-from-file \"%s\" %s %s --read-len %d "
> 
> 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.
> 
> Thanks,
> 
> J
> 
> 
> --
> Jason Greenbaum, Ph.D.
> Manager, Bioinformatics Core | jgbaum at liai.org
> La Jolla Institute for Allergy and Immunology
> 
> 
> 
> From: "Yarden Katz" <yarden at mit.edu>
> To: "J. Greenbaum" <jgbaum at liai.org>
> Cc: miso-users at mit.edu, "Lukas Chavez Wurm" <lchavez at liai.org>
> Sent: Wednesday, July 17, 2013 3:15:51 PM
> Subject: Re: [miso-users] MISO tests appear to be failing
> 
> Hi,
> 
> Could you please let me know which MISO version you are using?  Is it 0.4.9?
> 
> 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:
> 
> > python /share/apps/lib/python2.7/site-packages/misopy/index_gff.py ...
> 
> 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.
> 
> Could you please let me know what the output of these commands is?
> 
> $ /usr/bin/env python -v 
> $ python -v
> 
> Thanks. Best, --Yarden
> 
> 
> 
> On Jul 17, 2013, at 5:58 PM, J. Greenbaum wrote:
> 
> > Hi all,
> > 
> > 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.
> > 
> > Thanks in advance,
> > 
> > J
> > 
> > 
> > Output of test_miso.py:
> > [jgbaum at compute-0-6 site-packages]$ /share/apps/bin/python2.7 misopy/test_miso.py          
> > Testing fr-unstranded...
> > Checking read  f_read  against  +
> > Checking read  f_read  against  -
> > Checking read  r_read  against  +
> > Checking read  r_read  against  -
> > Testing fr-firststrand...
> > Testing fr-secondstrand...
> > .Testing conversion of SAM to BAM...
> > 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
> > Converting SAM to BAM...
> >   - 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
> > [samopen] SAM header is present: 35 sequences.
> > Sorting BAM file...
> >   - 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
> > Indexing BAM...
> >   - Executing: samtools index /share/apps/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
> > Conversion took 0.00 minutes.
> > .Testing gene-level Psi...
> > Testing GFF indexing of: /share/apps/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff
> > 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
> >   File "/share/apps/lib/python2.7/site-packages/misopy/index_gff.py", line 151
> >     with open(gff_filename) as gff_in:
> >             ^
> > SyntaxError: invalid syntax
> > 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 
> >   File "/share/apps/lib/python2.7/site-packages/misopy/run_events_analysis.py", line 123
> >     with open(batch_fname, "w") as batch_out:
> >             ^
> > SyntaxError: invalid syntax
> > .
> > ----------------------------------------------------------------------
> > Ran 3 tests in 0.177s
> > 
> > OK
> > 
> > 
> > Output of module_availability.py:
> > [jgbaum at compute-0-6 site-packages]$ /share/apps/bin/python2.7 misopy/module_availability.py
> > Looking for required Python modules..
> > Checking for availability of: numpy
> > Checking for availability of: scipy
> > Checking for availability of: json
> > Checking for availability of: matplotlib
> > Checking for availability of: pysam
> > All modules are available!
> > Looking for required executables..
> > Checking if samtools is available
> >   - samtools is available
> > Checking if bedtools is available
> >   - bedtools is available
> > 
> > 
> > Module/program versions:
> > pysam 0.7.4
> > numpy 1.6.1
> > scipy 0.9.0
> > matplotlib: 1.1.0
> > samtools: 0.1.18
> > bedtools: v2.16.2-zip-466a9f0
> > Python: 2.7
> > 
> > 
> > --
> > Jason Greenbaum, Ph.D.
> > Manager, Bioinformatics Core | jgbaum at liai.org
> > La Jolla Institute for Allergy and Immunology
> > 
> > 
> > 
> > _______________________________________________
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> > miso-users at mit.edu
> > http://mailman.mit.edu/mailman/listinfo/miso-users
> 
> 
> 