mmsplice couldn't output separate score of each kind of splice type

[zofieLin]

• MMSplice version: 0.2.8
• Python version: Python-3.6.8
• Operating System: Linux

Description

I use the mmsplice to do the prediction of splice variants, however, the output only contain 3 scores, that is "mmsplice_pathogenicity" "mmsplice_dse" and "mmsplice_dlogitPsi". I wonder if it can output the scores like "mmsplice_alt_acceptorIntron,mmsplice_alt_acceptor,mmsplice_alt_exon,mmsplice_alt_donor,mmsplice_alt_donorIntron" and so on.

What I Did

My prediction script is this: predictions = predict_all_table(model, dl, batch_size=1024, split_seq=False, assembly=True, pathogenicity=True, splicing_efficiency=True, progress=True) predictions.to_csv(out_csv)

My output is like this: ID,mmsplice_dlogitPsi,exons,mmsplice_pathogenicity,mmsplice_dse 0,17:41197805:ACATCTGCC:['A'],0.04854488531130818,17_41197646_41197819:-,0.9425130312488815,-0.003766304501151105

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[MuhammedHasan]

Hi @qf-Lin,

If you do not want to assemble modular score as a single score, you need to specify the argument assembly=False of predict_all_table. Then you will get each individual modular scores of MMSplice modules.

[zofieLin]

Hi @MuhammedHasan,

Thank you so much for your prompt response. Probably I misunderstand the function of "assembly". It is fine now, but, it is assembly=False and pathogenicity=True can't be process in the same time? When using assembly=False , I can't get the result of "mmsplice_pathogenicity".

Thank you.