YeoLab / YeoLab/rbp-maps

UnboundLocalError: local variable 'interval' referenced before assignment

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Python
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Description

I was able to install rbp-maps using Docker using the command docker pull brianyee/rbp-maps:a5c9bd9 (but not docker pull brianyee/rbp-maps). However, I was not able to successfully run plot_map using either --ipbam for plotting density or --peak for plotting peaks.

For HPC, I need to use singularity, and this was one of my calls:
singularity run rbpmaps.sif plot_map --peak <path_to_bigbed> --annotations <path_to_SE.MATS.JC.nonoverlap.txt> <path_to_HepG2_native_cassette_exons_all> --annotation_type rmats rmats --output <path_to_png> --event se --normalization_level 0 --testnums 0 --bgnum 1 --sigtest fisher

I received the following message:
Traceback (most recent call last):
File "/opt/conda/bin/plot_map", line 11, in
load_entry_point('rbp-maps==0.1.4', 'console_scripts', 'plot_map')()
File "/opt/conda/lib/python2.7/site-packages/rbp_maps-0.1.4-py2.7.egg/maps/plot_map.py", line 548, in main
File "/opt/conda/lib/python2.7/site-packages/rbp_maps-0.1.4-py2.7.egg/maps/plot_map.py", line 104, in run_make_peak
File "/opt/conda/lib/python2.7/site-packages/rbp_maps-0.1.4-py2.7.egg/density/Map.py", line 701, in create_matrices
File "/opt/conda/lib/python2.7/site-packages/rbp_maps-0.1.4-py2.7.egg/density/matrix.py", line 562, in skipped_exon
UnboundLocalError: local variable 'interval' referenced before assignment

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with density/matrix.py at skipped_exon, identified in the traceback, and reproduce the failure using the supplied plot_map --peak command. Check the related plot_map.py entry points for the --peak and --ipbam paths. Done means both plotting modes complete without the UnboundLocalError.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli, data-visualization
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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