Closed zofieLin closed 5 years ago
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.
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.
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