Nothing
gkmsvm_kernel <- function( posfile,
negfile,
outfile,
L=10,
K=6,
maxnmm=3,
maxseqlen=10000,
maxnumseq=1000000,
useTgkm=1,
alg=0,
addRC=TRUE,
usePseudocnt=FALSE,
wildcardLambda=1.0,
wildcardMismatchM=2,
alphabetFN="NULL"){
params = list(L=L,
K=K,
maxnmm=maxnmm,
maxseqlen=maxseqlen,
maxnumseq=maxnumseq,
useTgkm=useTgkm,
alg=alg,
addRC=addRC,
usePseudocnt=usePseudocnt,
OutputBinary=FALSE,
posfile=posfile,
negfile=negfile,
outfile=outfile,
wildcardLambda=wildcardLambda,
wildcardMismatchM=wildcardMismatchM,
alphabetFN=alphabetFN
);
# print(params)
## test for duplicate id
if (requireNamespace("seqinr", quietly = TRUE)){
posfn = posfile;
negfn = negfile;
pos = seqinr::read.fasta(posfn)
neg = seqinr::read.fasta(negfn)
if(length(which(duplicated(names(pos))))>0){
print(paste("Error: duplicated sequence ID in", posfn))
print(names(pos)[which(duplicated(names(pos)))])
stop("Error: duplicated sequence ID");
}
if(length(which(duplicated(names(neg))))>0){
print(paste("Error: duplicated sequence ID in", negfn))
print(names(neg)[which(duplicated(names(neg)))])
stop("Error: duplicated sequence ID");
}
if(length(which(duplicated(c(names(pos),names(neg)))))>0){
print(paste("Error: Same sequence ID found in positive and negative sets:", posfn, negfn))
print(c(names(pos),names(neg))[which(duplicated(c(names(pos),names(neg))))])
stop("Error: duplicated sequence ID");
}
}
invisible(.Call('gkmSVM_gkmsvm_kernel', PACKAGE = 'gkmSVM', params))
}
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