Resolve error running mesa ir_table

[hbeale]

The following error was encountered in my mesa verification runs as described here. Dennis recognizes the error and believes it has to do with filtering, i.e. there's a junction in active data that it's expecting to be in the dictionary but has been removed by filtering.

(splicedice_env) ubuntu@hbeale-mesa:/mnt/data/output/2024.10.03_15.53.30$ mesa ir_table -i ${out_prefix}_inclusionCounts.tsv -c ${out_prefix}_allClusters.tsv --coverageDirectory ${out_dir}/coverage/ --annotation $genes --outputPrefix ${out_prefix}
Gathering inclusion counts and clusters...
Calculating IR values...
Traceback (most recent call last):
  File "/mnt/scratch/splicedice/splicedice_env/bin/mesa", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/mnt/scratch/splicedice/splicedice_env/lib/python3.12/site-packages/mesa/__main__.py", line 59, in main
    args.main(args)
  File "/mnt/scratch/splicedice/splicedice_env/lib/python3.12/site-packages/mesa/ir_table.py", line 191, in run_with
    junctions, IR, RSD = calculateIR(samples,coverageDirectory,counts,clusters,annotated,args)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/scratch/splicedice/splicedice_env/lib/python3.12/site-packages/mesa/ir_table.py", line 140, in calculateIR
    if RSD[sample][junction] < args.RSDthreshold:
       ~~~~~~~~~~~^^^^^^^^^^
KeyError: 'chr21:45497661-45504010:+'
(splicedice_env) ubuntu@hbeale-mesa:/mnt/data/output/2024.10.03_15.53.30$ 

[hbeale]

after update, adding --makeRSDtable to ir_table command resolves the issue above. however, I encounted a new error: /mnt/scratch_2024.12.09_21.02.52/splicedice/splicedice_env8/lib/python3.12/site-packages/splicedice/ir_table.py:120: RuntimeWarning: invalid value encountered in scalar divide

next step

• consider making makeRSDtable a default
• create issue for RuntimeWarning: invalid value encountered in scalar divide