geno2proteo (version 0.0.6)

genomicLocsToWholeDNASequence: Obtaining the DNA sequences of a list of genomic loci

Description

The function takes a list of genomic loci and tries to find the whole DNA sequences within each of the loci.

Usage

genomicLocsToWholeDNASequence(inputLoci, DNAfastaFile, 
                                tempFolder = "./", perlExec='perl')

Arguments

inputLoci

A data frame containing the genomic loci as the input. Each row is for one genomic locus. The first column is the chromosome name, the 2nd and 3rd columns are the start and end coordinates of the locus in the chromosome, and the 4th column specifies the strand of chromosome ("+" and "-" for forward and reverse strand, respectively). Other columns are optional and will not be used by the function. Note that the chromosome name can be either in the ENSEMBL style, e.g. 1, 2, 3, …, and X, Y and MT, or in another popular style, namely chr1, chr2, chr3, …, and chrX, chrY and chrM. But they cannot be mixed in the input of one function call.

DNAfastaFile

The name of a fasta file containing the whole DNA sequence of the genome used. For details about this data file see the documentation of this package.

tempFolder

A temporary folder into which the program can write some temporary files which will be deleted when the function running is finished. The default value is the current folder.

perlExec

Its value should be the full path of the executable file which can be used to run Perl scripts (e.g. "/usr/bin/perl" in a linux computer or "C:/Strawberry/perl/bin/perl" in a Windows computer). The default value is "perl".

Value

The function returns a data frame containing the original genomic loci as in the input and after them, one additional column for the DNA sequence of the corresponding genomic locus.

Details

This function obtains the whole DNA sequences of a list of genomic loci. Note that, in contrast, another function genomicLocToProteinSequence in this package can return the DNA sequences of the coding regions within the given genomic loci.

Examples

# NOT RUN {
    dataFolder = system.file("extdata", package="geno2proteo")
    inputFile_loci=file.path(dataFolder, 
        "transId_pfamDomainStartEnd_chr16_Zdomains_22examples_genomicPos.txt")
    DNAfastaFile =  file.path(dataFolder, 
        "Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.gz")

    inputLoci = read.table(inputFile_loci, sep="\t", stringsAsFactors=FALSE)
    
    tmpFolder = tempdir()

    DNASeqNow = genomicLocsToWholeDNASequence(inputLoci=inputLoci, 
                            DNAfastaFile=DNAfastaFile, tempFolder=tmpFolder)

# }