netToAxt: netToAxt

Description

Wrapper function of netToAxt and axtSort: convert net (and chain) to axt, and sort axt files. This function doesn't work on Windows platform since Kent utilities only support Linux and Unix platform.

Usage

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")

Arguments

in.net

character(1): file names of input net file.

in.chain

character(1): file names of input chain file.

assemblyTarget

character(1): the file name of target assembly twoBit file.

assemblyQuery

character(1): the file name of query assembly twoBit file.

axtFile

character(1): file names of output axt file.

removeFiles

boolean: When TRUE, the input net and chain files will be removed after the conversion.

binaryNetToAxt

character(1): the name/filename of the binary netToAxt to call.

binaryAxtSort

character(1): the name/filename of the binary axtSort to call.

Value

character(1): the file name of output axt file.

References

http://hgdownload.cse.ucsc.edu/admin/exe/

Examples

Run this code

  ## 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)