shuffle_sequence truncated
Mjaraespejo opened this issue · comments
Hi, I am trying to use the shuffle_sequence function from the universalmotif package in order to shuffle a data containing ~19300 fasta sequeunces of 50 nt length. When I run my script using jus 10 sequences it works perfectly, but when I tried to used with the big data I get this error message :
fastaFile = readDNAStringSet("m6A_5-3-sequences.fasta")
euler <- shuffle_sequences(fastaFile, k = 2, method = "euler")
Error in edgematrix[i, alph.i[lastlets[[i]]]] :
incorrect number of dimensions
Hmm. Would you mind trying the development version? The internal shuffle_sequences() code has been completely rewritten.
BiocManager::install("universalmotif", version = "devel")
If this still doesn't work, please send me some example sequences which trigger this error. If I were to guess, it has to do with unrecognised characters, but it's hard to tell without seeing the fasta file.
New Bioconductor release, which means your question is likely now outdated. Feel free to reopen if you still run into problems with the new version.