CNEr (version 1.8.3)

lavToPsl: lavToPsl

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 platform.

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.

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)