[miso-users] Followup to: Syntax error with MISO

[Yarden Katz]

Hi Larry,

Since miso just calls "python" internally, a simpler trick that would not require altering the source would be to put MISO first in your PATH environment variable.  E.g.

$ export PATH=/your/python/path/python2.7:$PATH

(if you're using sh), which should make sure that the Python you get by invoking python is the one you expect, and not the system default.

 --Yarden



On Jul 29, 2013, at 11:12 PM, Singh, Larry (NIH/NHGRI) [E] wrote:

> Hi Yarden,
> 
> I was having a similar problem as the user below reported in the archives about a Syntax error with MISO.  I soon realized that the older version of python was being used, as there were two versions on my system.  Python 2.4 gives a syntax error, python 2.7 doesn't.  To get around this I edited run_events_analysis.py and changed lines 151 and 562 to put the full path for python in the miso_cmd variable.  I'm not sure if the user was still having this problem, but this workaround did the trick for me.
> 
> Best regards,
> -Larry.
> 
> Katerina Bendak katschib at gmx.de <mailto:miso-users%40mit.edu?Subject=%5Bmiso-users%5D%20Syntax%20error%20with%20MISO&In-Reply-To=>
> Tue Mar 5 21:35:49 EST 2013
> 
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> 
> ________________________________
> 
> Dear Yarden,
> 
> 
> 
> I have only just started using MISO and am not very experienced with
> bioinformatics. I have mapped my RNA-seq data with TOPHAT and am currently
> trying to detect differentially spliced exons with MISO. The program
> unfortunately seems to run into a syntax error. I pasted everything below.
> Maybe you have an idea what could be going wrong?
> 
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