[miso-users] miso_logger error

[Yarden Katz]

Hi Helena,

You're right about the error and about the fix.  It was fixed in github on dev branch (https://github.com/yarden/MISO/compare/dev) and will get incorporated into next release.

Best, Yarden

On Apr 20, 2015, at 10:31 AM, Helena Storvall <Helena.Storvall at ki.se> wrote:

> Hi Yarden and MISO-users,
> I encountered an error in MISO (version 0.5.3) that was also described recently by Ankit Arora.
> I couldn't figure out how to reply to the old thread, but I think I have found the source of the error and thought I should share so it can be fixed for next release.
> 
> The error message looks like the following:
> 
> Traceback (most recent call last):
> 
>   File "/usr/local/bin/miso", line 9, in <module>
> 
>     load_entry_point('misopy==0.5.3', 'console_scripts', 'miso')()
> 
>   File "/usr/local/lib/python2.7/dist-packages/misopy/miso.py", line 591, in main
> 
>     wait_on_jobs=wait_on_jobs)
> 
>   File "/usr/local/lib/python2.7/dist-packages/misopy/miso.py", line 372, in compute_all_genes_psi
> 
>     given_read_len=read_len)
> 
>   File "/usr/local/lib/python2.7/dist-packages/misopy/run_events_analysis.py", line 171, in check_gff_and_bam
> 
>     miso_logger.warning("It looks like your GFF annotation file and your BAM " \
> 
> NameError: global name 'miso_logger' is not defined
> 
> 
> 
> I know that this occurs because the chromosomes in the beginning of my bam-files does not have the "chr" prefix, while those in the beginning of the gff file do. However, this should not crash the script, only print a warning and continue. Looking closer into the source code of run_events_analysis.py I can see that a logger object is input into the function and given the variable name "main_logger".  In the section where mismatches between the files are handled, "miso_logger" is used instead which is not defined anywhere in the script. I changed "miso_logger" to "main_logger" in the code, and now MISO runs perfectly.
> 
> 
> 
> Best regards,
> 
> Helena Storvall
> 
> 
> 
> 
> 
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