geno2proteo (version 0.0.6)

generatingCDSaaFile: Generating a file containing the DNA and AA sequences of all the protein coding regions (CDSs) in a genome

Description

This function will find the DNA and protein sequences for each CDS region listed in the ENSEMBL gene annotation file (gtf file) provided, and store the CDS regions and the corresponding DNA and protein sequences in an output data file. The output data file will be needed by some of the functions in this package.

Usage

generatingCDSaaFile(geneticCodeFile_line, gtfFile, DNAfastaFile, 
outputFolder = "./", perlExec='perl')

Arguments

geneticCodeFile_line

A text file containing a genetic coding table of the codons and the amino acids coded by those codons. A file containing the standard genetic coding table is provided in this package, which is the file ‘geneticCode_standardTable_lines.txt’ in the folder "geno2proteo/extdata/" which will be located in the folder that you install the package. This will be available after you have installed the package.

Alternatively you can create your own genetic table if needed. The format of the genetic table used in this package is one line for one codon. The first column is the codon (namely 3 DNA letters) and the second column is the name (in a single letter) of the amino acid coded by the codon. You may have more columns if you want but only the first two columns are used by the package, and the columns are separated by a tab.

gtfFile

A text file in GTF format containing the gene annotations of the species that you are interested in. You may obtain this file from the ENSEMBL web site. The text file can be compressed by GNU Zip (e.g. gzip). For the details about how to get the data file from ENSEMBL web site, see the documentation of this package.

DNAfastaFile

A text file in fasta format containing the DNA sequence for the genome that you want to use for analysing the data. The text file can be compressed by GNU Zip (e.g. gzip). You may download the file directly from the ENSEMBL web site. For the details about how to get the data file from ENSEMBL web site, see the documentation of this package.

outputFolder

A folder where the result file will be stored. 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

This function does not return any specific value but generates a file in the output folder containing the DNA and AA sequences of the CDS regions. The first part of the name of the result file is same as the gene annotation file (namely the gtf file), and the last part is ‘_AAseq.txt.gz’.

Details

This function generates a data file containing the genomic locations, DNA sequences and protein sequences of all of the coding regions (CDSs), which will be used by some of other functions in this packages.

Examples

# NOT RUN {
    # the data folder in this package
    dataFolder = system.file("extdata", package="geno2proteo") 

    geneticCodeFile_line = file.path(dataFolder, 
                                    "geneticCode_standardTable_lines.txt")
    gtfFile = file.path(dataFolder, 
                "Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz")
    DNAfastaFile =  file.path(dataFolder, 
            "Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.gz")
    
    outputFolder = tempdir(); # using the current folder as output folder
    # calling the function.
    generatingCDSaaFile(geneticCodeFile_line=geneticCodeFile_line, 
        gtfFile=gtfFile, DNAfastaFile=DNAfastaFile, outputFolder=outputFolder)
    
    filename00 = sub(".*/", "", gtfFile)
    # get the output file's name.
    outputFile = paste(outputFolder, "/", filename00, "_AAseq.txt.gz", sep="")
    # read the content of the output file into a data frame.
    aaSeq = read.table(outputFile, sep="\t", stringsAsFactors=FALSE)

# }