lastal {CNEr} | R Documentation

## lastal wrapper

### Description

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

### Usage

      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

      ## 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)

[Package CNEr version 1.18.1 Index]