genome_addSequence: Add genome sequence on Fasta format to 'genomebrowser'.

In D3GB: Interactive Genome Browser with R

Description

genome_addSequence add FASTA sequences to genomeviewer.

Usage

genome_addSequence(gb, fastafile)

Arguments

gb	a genome browser object produced by the function genomebrowser.
fastafile	a "character" string representing the input Fasta file to be added in the genome browser.

Value

The function add genome sequence on Fasta format to genomebrowser.

Author(s)

David Barrios and Carlos Prieto. Bioinformatics, University of Salamanca. See http://d3gb.usal.es/

See Also

The ‘D3GB’ Website: http://d3gb.usal.es

genomebrowser, genome_addGFF, genome_addTrack, genome_addVCF.

Examples

## Not run: 
# Download fasta file
fasta <- tempfile()
download.file(paste0("ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/297/395/",
"GCF_000297395.2_ASM29739v2/GCF_000297395.2_ASM29739v2_genomic.fna.gz"),fasta)

# Genome browser generation.
# It creates a genome browser ready to be viewed in Firefox.
# For a server version, ready to be shared with Apache as a Website, set the parameter server=True
gb <- genomebrowser(getAssemblyFromFasta(fasta), dir = "Micromonospora_sequence")

genome_addSequence(gb,fasta)

## End(Not run)

D3GB documentation built on May 2, 2019, 9:42 a.m.