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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