netToAxt {CNEr} | R Documentation |
Wrapper function of netToAxt
and axtSort
:
convert net (and chain) to axt, and sort axt files.
This function doesn't work on the Windows platform since Kent utilities only
support Linux and Unix platforms.
netToAxt(in.net, in.chain, assemblyTarget, assemblyQuery, axtFile=paste0(sub("\\.2bit$", "", basename(assemblyTarget), ignore.case = TRUE), ".", sub("\\.2bit$", "", basename(assemblyQuery), ignore.case = TRUE), ".net.axt"), removeFiles=FALSE, binaryNetToAxt="netToAxt", binaryAxtSort="axtSort")
in.net |
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in.chain |
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assemblyTarget |
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assemblyQuery |
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axtFile |
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removeFiles |
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binaryNetToAxt |
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binaryAxtSort |
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character
(1): the file name of output axt file.
Ge Tan
http://hgdownload.cse.ucsc.edu/admin/exe/
## Not run: ## This example doesn't run because it requires two bit files and external ## Kent utilities. in.net <- file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt", "danRer10.hg38.noClass.net") in.chain <- file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt", "danRer10.hg38.all.pre.chain") assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit" assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit" netToAxt(in.net, in.chain, assemblyTarget, assemblyQuery, axtFile=file.path("/Users/gtan/OneDrive/Project/CSC/CNEr/axt", paste0(sub("\\.2bit$", "", basename(assemblyTarget), ignore.case = TRUE), ".", sub("\\.2bit$", "", basename(assemblyQuery), ignore.case = TRUE), ".net.axt")), removeFiles=FALSE, binaryNetToAxt="netToAxt", binaryAxtSort="axtSort") ## End(Not run)