getAssemblyFromFasta: Create an assembly from a FASTA file for its use as parameter...

In D3GB: Interactive Genome Browser with R

Description

getAssemblyFromFasta create assemblies from a FASTA file for their use as parameter of genomebrowser or genomemap.

Usage

getAssemblyFromFasta(fasta)

Arguments

fasta

a "character" string representing the input Fasta file to be added in the genome browser.

Value

a data frame in BED format ready to use as an assembly in genomebrowser or genomemap.

Note

FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes.

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, genomemap.

Examples

# 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)

# Assembly generation
getAssemblyFromFasta(fasta)

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