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 <[email protected]> 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 > > > > > > _______________________________________________ > miso-users mailing list > [email protected] > http://mailman.mit.edu/mailman/listinfo/miso-users
smime.p7s
Description: S/MIME cryptographic signature
_______________________________________________ miso-users mailing list [email protected] http://mailman.mit.edu/mailman/listinfo/miso-users
