importFA: Importing a Fasta File.

In fischuu/GenomicTools.fileHandler: File Handlers for Genomic Data Analysis

Importing a Fasta File.

Description

This function imports a standard fasta file

Usage

importFA(file, toupper = TRUE, verbose = TRUE)

Arguments

file	Specifies the filename/path
toupper	Logical, input sequence will to rewriten to capital letters only
verbose	Logical, verbose function output

Details

This function imports a standard fasta file. Hereby, it does not matter if the identifier and sequence are alternating or not, as the rows starting with '>' are used as identifer.

The example file was downloaded from here and was then further truncated respective transformed to fasta format:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/sequence_read/

Value

An object of class fa containing the sequences. The names correspond to the sequence names given in the fasta file.

Author(s)

Daniel Fischer

See Also

print.fa, summary.fa

Examples

 # Define here the location on HDD for the example file
   fpath <- system.file("extdata","example.fasta", package="GenomicTools.fileHandler")
 # Import the example fasta file  
   fastaFile <- importFA(file=fpath)
 

fischuu/GenomicTools.fileHandler documentation built on Feb. 15, 2025, 1:11 p.m.