search pattern(s) in a genome

Description

internal function for searching pattern(s) in a genome used by buildREmap leveraging BSgenome package

Usage

searchPattern(dict0, BSgenomeName, outfile = "")

Arguments

Value

results are saved in the file specified by outfile

Author(s)

Lihua Julie Zhu

References

http://bioconductor.org/packages/2.8/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf

See Also

buildREmap

Examples

	library(REDseq)
	patternFile = system.file("extdata", "examplePattern.fa", package="REDseq")
	example.dict0 <- readDNAStringSet(patternFile, "fasta")
	library(BSgenome.Celegans.UCSC.ce2)
	REDseq:::searchPattern(dict0 = example.dict0, BSgenomeName=Celegans, outfile=tempfile())

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(REDseq)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: BSgenome.Celegans.UCSC.ce2
Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Loading required package: multtest
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ChIPpeakAnno
Loading required package: grid
Loading required package: VennDiagram
Loading required package: futile.logger

No methods found in "IRanges" for requests: %in%
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/REDseq/searchPattern.Rd_%03d_medium.png", width=480, height=480)
> ### Name: searchPattern
> ### Title: search pattern(s) in a genome
> ### Aliases: searchPattern
> ### Keywords: internal
> 
> ### ** Examples
> 
> 	library(REDseq)
> 	patternFile = system.file("extdata", "examplePattern.fa", package="REDseq")
> 	example.dict0 <- readDNAStringSet(patternFile, "fasta")
> 	library(BSgenome.Celegans.UCSC.ce2)
> 	REDseq:::searchPattern(dict0 = example.dict0, BSgenomeName=Celegans, outfile=tempfile())
>>> Finding all hits in sequences chrI ...
>>> DONE searching
>>> Finding all hits in sequences chrII ...
>>> DONE searching
>>> Finding all hits in sequences chrIII ...
>>> DONE searching
>>> Finding all hits in sequences chrIV ...
>>> DONE searching
>>> Finding all hits in sequences chrV ...
>>> DONE searching
>>> Finding all hits in sequences chrX ...
>>> DONE searching
>>> Finding all hits in sequences chrM ...
>>> DONE searching
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>