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genomicLocsToWholeDNASequence <-
function(inputLoci, DNAfastaFile, tempFolder='./', perlExec='perl') {
scriptFolder= system.file("exec", package="geno2proteo")
# the perl script used to get the DNA for the CDS from the fasta file.
perlScript_getDNAseq=file.path(scriptFolder,
"getDNAseqsFromGenome_loci.perl")
# get the genomic loci
loci_0 = inputLoci
if(!is.data.frame(loci_0)) loci_0 = data.frame(loci_0,
stringsAsFactors=FALSE)
loci_0[,1] = as.character(loci_0[,1]);
loci_0[,2] = as.numeric(as.character(loci_0[,2]));
loci_0[,3] = as.numeric(as.character(loci_0[,3]))
# make sure that the original loci were named by their row index.
rownames(loci_0) = 1:nrow(loci_0)
# removing those loci which don't have a proper location.
kk = is.na(loci_0[,1:4]); kk = rowSums(kk)>0;
loci = loci_0[!kk,]
if(nrow(loci)==0) {
return("there is no valid loci!!")
}
filenamePrefix = 'inputFile_loci'
filenameGenomicLoc= paste(tempFolder, '/',
filenamePrefix, '_genomicLoc.txt', sep='');
write.table(loci, file=filenameGenomicLoc, sep='\t', quote=FALSE,
row.names=FALSE, col.names=FALSE)
# then run the perl script to get the DNA sequence of the regions
filenameDnaSeq = paste(tempFolder, '/', filenamePrefix,
'_genomicLoc_DNAseq.txt', sep='');
DNAfastaFile00 = DNAfastaFile
# uncompress the fasta file, not remove the compressed
if(grepl('\\.gz$', DNAfastaFile)[1]) {
#R.utils::gunzip(DNAfastaFile, remove=FALSE)
#DNAfastaFile = sub('\\.gz$','', DNAfastaFile)
destName=paste(tempFolder, '/',
sub('.gz$', '', sub('.*\\/', '', DNAfastaFile)), sep='')
R.utils::decompressFile(filename=DNAfastaFile, destname=destName,
ext='gz', FUN=gzfile, remove=FALSE)
DNAfastaFile = destName;
}
command = paste('"', perlExec, '" "', perlScript_getDNAseq, '" "',
filenameGenomicLoc, '" "',DNAfastaFile, '" "',filenameDnaSeq, '"', sep='')
system(command)
if(grepl('\\.gz$', DNAfastaFile00)[1]) { # if uncompressed the fasta file
if (file.exists(DNAfastaFile)) { invisible(file.remove(DNAfastaFile))}
DNAfastaFile= DNAfastaFile00
}
lociExt = read.table(filenameDnaSeq, sep='\t', stringsAsFactors=FALSE)
kk = rep('NA', nrow(loci_0))
kk[as.numeric(rownames(loci))] = lociExt[,ncol(lociExt)]
# append the DNA seq to the end of the row.
lociExt_0 = cbind(loci_0, DNAseq = kk)
# removing the tempory files
fn=filenameGenomicLoc; if (file.exists(fn)) invisible(file.remove(fn))
fn=filenameDnaSeq; if (file.exists(fn)) invisible(file.remove(fn))
lociExt_0
}
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