[miso-users] MISO tests appear to be failing

Wed Jul 17 19:08:19 EDT 2013

Hi Yarden, 

Thanks for the clarification. Sorry I misread your original message. 

-J 

-- Jason Greenbaum, Ph.D. 
Manager, Bioinformatics Core | jgbaum at liai.org 
La Jolla Institute for Allergy and Immunology 

----- Original Message -----

> 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 3:49:08 PM
> Subject: Re: [miso-users] MISO tests appear to be failing

> 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
> > >
> > >
> > >
> > > _______________________________________________
> > > miso-users mailing list
> > > miso-users at mit.edu
> > > http://mailman.mit.edu/mailman/listinfo/miso-users
> >
> >
> >
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