voila modulize error on .psicov

[Maoting Chen]

Hi San,

I tried to run voila modulize on .psicov to get the AS event types on different conditions. Below is how I got the .psicov and .sgc file and ran voila modulize: 

majiq psi-coverage ../build_4rep_group_majiq-files/splicegraph.zarr ./psi_coverage_4rep_sep_group/OP.psicov ../build_4rep_group_majiq-files/OP1.Aligned.out.sj ../build_4rep_group_majiq-files/OP2.Aligned.out.sj ../build_4rep_group_majiq-files/OP7.Aligned.out.sj ../build_4rep_group_majiq-files/OP8.Aligned.out.sj --prefixes OP1 OP2 OP7 OP8 

majiq-v3 sg-coverage ./build_4rep_group_majiq-files/splicegraph.zarr ./sg-coverage_4rep_group/OP.sgc ./build_4rep_group_majiq-files/OP1.Aligned.out.sj ./build_4rep_group_majiq-files/OP2.Aligned.out.sj ./build_4rep_group_majiq-files/OP7.Aligned.out.sj ./build_4rep_group_majiq-files/OP8.Aligned.out.sj --prefixes OP1 OP2 OP7 OP8  (Note: no sg-coverage in majiq but only in majiq-v3)

voila modulize ../build_4rep_group_majiq-files/splicegraph.zarr ./psi_coverage_4rep_sep_group/OP.psicov ../sg-coverage_4rep_group/OP.sgc -d OP_modulize/ --show-all 

The error was reported: trying to get bins and more than one group returned, this should not happen Traceback (most recent call last): File "/n/home09/mtchen/.conda/envs/majiqV3/lib/python3.12/site-packages/rna_voila/classify.py", line 104, in classify_gene writer.alt5prime() File "/n/home09/mtchen/.conda/envs/majiqV3/lib/python3.12/site-packages/rna_voila/classifier/tsv_writer.py", line 783, in alt5prime quants = [event_non_changing, event_changing] + cases_non_changing + cases_changing + self.quantifications(module, 's', edge=event['Proximal']) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/n/home09/mtchen/.conda/envs/majiqV3/lib/python3.12/site-packages/rna_voila/classifier/quantification_finder.py", line 75, in quantifications quants = self.quantifications_int[field][0](*self.quantifications_int[field][1:])(lsv_id, edge) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/n/home09/mtchen/.conda/envs/majiqV3/lib/python3.12/site-packages/rna_voila/classifier/quantification_finder.py", line 188, in f return self._inner_edge_aggregate(lsv, generate_variances([lsv.bins][0]), edge) ^^^^^^^^ File "/n/home09/mtchen/.conda/envs/majiqV3/lib/python3.12/site-packages/rna_voila/api/view_matrix_zarr.py", line 453, in bins assert False ^^^^^ AssertionError Processing Genes and Modules [0/1]^M

However, if I ran voila modulize on .voila from majiq deltapsi and the two corresponding .sgc files, there was no problem.

I am using Voila v3.0.17.dev1+g11dc0f550. Could you please kindly help to look into this error? Happy to provide any other information needed.

Thank you,

Maoting

[San Jewell]

Hi Maoting, 

I believe that this was an issue with an untested combination of file/experiment grouping in voila, which was fixed in a recent update. (following the same pip command you used before should show version "voila 3.0.18.dev1+g69f22130d") ; if not, please let me know and I will check deeper into the cause. 

Thanks, 

-San

[Maoting Chen]

Hi San,

The issue was indeed solved after I installed the newest majiq and voila. Thank you for your clarification. 

I checked my gene of interest in the output of modulize result and want to ask how modulize define each AS event. One LSV of interest is defined as"other" in the modulize output, while I personally will think it is alternative first exon. Please see the attached splicegraph and the LSV of interest is gene:WBGene00018514:t:5793996-5794065. Could you please explain the inconsistency of modulize output and human judgement?

Thank youm

maoting