## ----代码，echo = false --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------代码< - function（...）{cat（paste（...，sep =“ \ n”））} date =“ r doc_date（）`“ pkg =”`r pkg_ver（'biocStyle'）`## --------------------------------------------------------------------------------------------------------------------------- # ## lastz aligner # assemblyDir <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit“＃axtDir < - ”/users/gtan/oneedrive/project/csc/cner/axt“＃assemblyTarget <-file.path（system.file（“ extdata”，＃package =“ bsgenome.drerio.ucsc.danrer10”），＃“ single_scepences.2bit”）＃assemblyQueryQuery <-file.path（system.file（“ extdata”，＃package =“ bsgenome.hsapiens.ucsc.hg38”），＃“ single_sporences.2bit”）（assemblyTarget，assemblyQuery，＃outputdir = axtDir，＃chrstarget = c（“ chr1”，“ chr2”，“ chr3”），＃chrsquery = c（“ chr1”，“ chr2”，“ chr2”，“ chr3”），＃distance =“”far”，mc.cores = 4）＃＃＃## lav文件转换为psl文件转换＃psls <-avtopsl（lavs，removelav = false，binary =“ lavtopsl”）## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------= true ------------------------------------------------------------------------------- ##构建LastDB索引＃System2（命令=“ LastDB”，args = C（“ - C”，file.path（assemblyDir，“ danrer10”），＃file.path（assemblyDir，“ danrer10.fa”）））＃## ##运行last Aligner＃lastAl（db = file.path（assemblyDir，“ danrer10”），＃queryfn = file.path（assemblyDir，'hg38.fa）“），＃outputfn = file.path（axtDir，“ danrer10.hg38.maf”），＃distance =“ far”，binary =“ last”，mc.cors = 4L）＃## ## maf to psl＃psls <-file.path（axtDir，“ danrer10.hg38.psl”）＃system2（command =“ maf-convert”，args = c（“ psl”，＃file.path（axtdir，“ danrer10.hg38.maf”），＃“>”，PSLS））## ----链，eval = false，echo = true --------------------------------------------------------------------------------------------------------------------------------------------------------- ##加入关闭对齐＃链<-AxtChain（psls，assemblyTarget = assemblyTarget，＃assemblyQuery = assemblyQuery = assemblyQuery，distancequery，danceblyquery，danceblyquery，dance =“ far”，＃emoverpsl =FALSE, binary="axtChain") # # ## Sort and combine # allChain <- chainMergeSort(chains, assemblyTarget, assemblyQuery, # allChain=file.path(axtDir, # paste0(sub("\\.2bit$", "", basename(assemblyTarget), # ignore.case=TRUE), ".", # sub("\\.2bit$", "", basename(assemblyQuery), # ignore.case=TRUE), ".all.chain")), # removeChains=FALSE, binary="chainMergeSort") ## ----netting, eval=FALSE, echo=TRUE------------------------------------------- # ## Filtering out chains # allPreChain <- chainPreNet(allChain, assemblyTarget, assemblyQuery, # allPreChain=file.path(axtDir, # paste0(sub("\\.2bit$", "", # basename(assemblyTarget), # ignore.case = TRUE), ".", # sub("\\.2bit$", "", # basename(assemblyQuery), # ignore.case = TRUE), # ".all.pre.chain")), # removeAllChain=FALSE, binary="chainPreNet") # # ## Keep the best chain and add synteny information # netSyntenicFile <- chainNetSyntenic(allPreChain, assemblyTarget, assemblyQuery, # netSyntenicFile=file.path(axtDir, # paste0(sub("\\.2bit$", "", # basename(assemblyTarget), # ignore.case = TRUE), ".", # sub("\\.2bit$", "", # basename(assemblyQuery), # ignore.case = TRUE), # ".noClass.net")), # binaryChainNet="chainNet", binaryNetSyntenic="netSyntenic") ## ----axtNet, eval=FALSE, echo=TRUE-------------------------------------------- # netToAxt(netSyntenicFile, allPreChain, assemblyTarget, assemblyQuery, # axtFile=file.path(axtDir, # paste0(sub("\\.2bit$", "", # basename(assemblyTarget), # ignore.case = TRUE), ".", # sub("\\.2bit$", "", # basename(assemblyQuery), # ignore.case = TRUE), # ".net.axt")), # removeFiles=FALSE, # binaryNetToAxt="netToAxt", binaryAxtSort="axtSort") # ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()