lastal wrapper

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Description

Wrapper function of lastal to do the pairwise whole genome alignment. This function doesn't work on Windows platform.

Usage

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  lastal(db, queryFn,
         outputFn=sub("\\.(fa|fasta)$", ".maf", 
                      paste(basename(db), basename(queryFn), sep = ","),
                      ignore.case = TRUE),
         distance=c("far", "medium", "near"), binary="lastal",
         mc.cores=getOption("mc.cores", 2L), echoCommand=FALSE)

Arguments

db

character(1): the file name of target assembly's lastal index.

queryFn

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

outputFn

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

distance

It can be "far", "medium" or "near". It decides the score matrix used in lastz aligner. See '?scoringMatrix' for more details.

binary

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

mc.cores

integer(1): the number of threads to use. By default, getOption("mc.cores", 2L).

echoCommand

boolean(1): When TRUE, only the command to run lastal is returned.

Value

A character(1) vector of ouput maf file names.

Note

lastal aligner must be installed on the machine to use this function.

Author(s)

Ge Tan

References

http://last.cbrc.jp/

See Also

lastz

Examples

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  ## Not run: 
    assemblyDir <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit"
    ## Build the lastdb index
    system2(command="lastdb", args=c("-c", file.path(assemblyDir, "danRer10"),
                                     file.path(assemblyDir, "danRer10.fa")))

    ## Run lastal aligner
    lastal(db=file.path(assemblyDir, "danRer10"),
         queryFn=file.path(assemblyDir, "hg38.fa"),
         outputFn=file.path(axtDir, "danRer10.hg38.maf"),
         distance="far", binary="lastal", mc.cores=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))
  
## End(Not run)

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