[miso-users] miso_logger error

[Helena Storvall]

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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