[miso-users] MISO tests appear to be failing

Wed Jul 17 18:33:29 EDT 2013

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 

----- 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 3:15:51 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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