YAMDA

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I have successfully tested YAMDA searching motifs in the test DNA dataset. Then I tried to run YAMDA with aminoacidic data (like an example in attached logo figure) with obvious...

StLeonidas

max_log_likelihoods, max_log_likelihoods_index = log_likelihoods.max(dim=0) IndexError: max(): Expected reduction dim 0 to have non-zero size.

1

python3 ./YAMDA/YAMDA-0.1/run_em.py -f 0.1 -r -e -w 20 -maxs 20000 -i ./raw_data/positive_sequence/R5_LUNG_M_2_positive_seq_uniq_name.fa -j ./raw_data/negtive_sequence/R5_LUNG_M_2_negtive_seq_uniq_name_paired.fa -oc ./motif_find/R5_output/LUNG Loading sequences from FASTA Searching positive sequences: 100%|███████████████████████████████████████████████████████████████████| 9/9 [00:02

Jean497

Keep finding the same motif

12

I asked for 10 motifs with -n 10, and found the same exact motif 10 times. Am I missing something here?

littleblackfish

This one requires actually doing some testing to see if it still works. I just used `pyximport` to see if it could automatically compile to C, it can without error,...

darkhipo