lavToPsl: lavToPsl

In CNEr: CNE Detection and Visualization

Description

Wrapper function of lavToPsl: Convert blastz lav to psl format. This function doesn't work on Windows platform since Kent utilities only support Linux and Unix platforms.

Usage

  lavToPsl(lavs, psls=sub("\\.lav$", ".psl", lavs, ignore.case = TRUE),
           removeLav=TRUE, binary="lavToPsl")

Arguments

lavs	character(n): file names of input lav files.
psls	codecharacter(n): file names of output psl files. By default, in the same folder of input lav files with same names.
removeLav	boolean: When TRUE, the input lavs files will be removed after the conversion.
binary	character(1): the name/filename of the binary lavToPsl to call.

Value

character(n): the file names of output psl files.

Author(s)

Ge Tan

References

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

See Also

lastz

Examples

  ## Not run: 
  ## This example doesn't run because it requires lav files from previous steps 
  ## and external Kent utilities.
    lavs <- tools::list_files_with_exts(
              dir="/Users/gtan/OneDrive/Project/CSC/CNEr/axt", exts="lav")
    lavToPsl(lavs, removeLav=FALSE, binary="lavToPsl")
  
## End(Not run)

CNEr documentation built on Nov. 8, 2020, 5:36 p.m.