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YeoLab / rbp-maps

splicing and feature maps for RBPs
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UnboundLocalError: local variable 'interval' referenced before assignment #11

Open J9DM opened 2 years ago

J9DM commented 2 years ago

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

byee4 commented 2 years ago

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

Assuming is one of the files downloaded from here, could you try to see if this command runs? In other words, replace the second 'rmats' with 'tab' since the background control files were not generated with rMATS:

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 tab --output <path_to_png> --event se --normalization_level 0 --testnums 0 --bgnum 1 --sigtest fisher