Nothing
generate_enzyme_file<-function(enzyme="HindIII",enzymesite="AAGCTT",chrom_file="chrom_hg19.sizes",enzymedir="annotation",enzymeoverhangs5=1,genomeName="hg19")
{
chrom_info=read.table(chrom_file,fill=TRUE, stringsAsFactors=FALSE)
extdata_file=system.file("extdata", package="HBP")
all_genomedb=read.csv(paste(extdata_file,"/all_genome_db.csv",sep = ""),header=FALSE)
enzymesitesfile=paste(enzyme,"_resfrag_",genomeName,".bed",sep="")
enzyme_dir=list.files(path=enzymedir,full.names=F,pattern=enzymesitesfile)
if(length(enzyme_dir)==0)
{
for(i in 1:length(all_genomedb))
{
dbfind=-1
dbrequire=FALSE
r_genomedb=NULL
dbfind=regexpr(genomeName,all_genomedb[1,i])
if(dbfind!=-1)
{
r_genomedb=as.character(all_genomedb[1,i])
dbrequire=require(all_genomedb[1,i],character.only = TRUE)
break
}
}
if(!is.null(r_genomedb))
{
if(dbrequire==FALSE)
{
print(paste("try to install the R package ",r_genomedb,sep=""))
source("http://www.bioconductor.org/biocLite.R")
biocLite(r_genomedb)
}else
{
all_chr <- chrom_info[,1]
resFrag <- getRestrictionFragmentsPerChromosome(resSite=enzymesite, chromosomes=all_chr, overhangs5=enzymeoverhangs5, genomePack=r_genomedb)
allRF <- do.call("c",resFrag)
names(allRF) <- unlist(sapply(resFrag, function(x){paste0("HIC_", seqlevels(x), "_", 1:length(x))}))
if(file.exists(enzymedir)==FALSE)
{
dir.create(enzymedir)
}
export(allRF, format="bed", con=paste(enzymedir,"/",enzymesitesfile,sep=""))
}
}else
{
print(paste("can not find the genome file",sep=""))
}
}else
{
print(paste("enzymesites file ",enzymesitesfile," is already existed, skip to generate it"))
}
}
run_hicpro<-function(hicpro_path="HiC-Pro",inputfile="rawdata",configfile="config-hicpro",outdir="hg19")
{
hiccmd=paste(hicpro_path," -i ",inputfile," -o ",outdir," -c ",configfile,sep="")
print(hiccmd)
system(hiccmd)
}
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