Nothing
gkmsvm_classify <- function( seqfile,
svmfnprfx,
outfile,
L=10,
K=6,
maxnmm=3,
maxseqlen=10000,
maxnumseq=1000000,
useTgkm=1,
alg=0,
addRC=TRUE,
usePseudocnt=FALSE,
batchSize=100000,
wildcardLambda=1.0,
wildcardMismatchM=2,
alphabetFN="NULL",
svseqfile=NA,
alphafile=NA){
if(is.na(svseqfile)){
svseqfile= paste(svmfnprfx, 'svseq.fa', sep='_')
alphafile= paste(svmfnprfx, 'svalpha.out', sep='_')
}
## test duplicate names in .fa file:
if (requireNamespace("seqinr", quietly = TRUE)){
snams = names(seqinr::read.fasta(seqfile))
if(length(which(duplicated(snams)))>0){
print(paste("Error: duplicated sequence IDs in", seqfile))
stop("Error: duplicated sequence ID");
}
}
params = list(seqfile=seqfile,
svseqfile=svseqfile,
alphafile=alphafile,
outfile=outfile,
L=L,
K=K,
maxnmm=maxnmm,
maxseqlen=maxseqlen,
maxnumseq=maxnumseq,
useTgkm=useTgkm,
alg=alg,
addRC=addRC,
usePseudocnt=usePseudocnt,
batchSize=batchSize,
wildcardLambda=wildcardLambda,
wildcardMismatchM=wildcardMismatchM,
alphabetFN=alphabetFN
);
# print(params)
invisible(.Call('gkmSVM_gkmsvm_classify', PACKAGE = 'gkmSVM', params))
}
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