MAGNAMWAR (version 2.0.4)

FormatMCLFastas: Format all raw GenBank fastas to single OrthoMCL compatible fasta file

Description

Creates the composite fasta file for use in running OrthoMCL and/or submitting to www.orthomcl.org

Usage

FormatMCLFastas(fa_dir, genbnk_id = 4)

Arguments

fa_dir

Path to the directory where all raw GenBank files are stored. Note, all file names must be changed to a 4-letter code representing each species and have '.fasta' file descriptor

genbnk_id

(Only necessary for the deprecated version of fasta headers) The index of the sequence ID in the GenBank pipe-separated annotation line (default: 4)

Value

Returns nothing, but prints the path to the final OrthoMCL compatible fasta file

Examples

# NOT RUN {
dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
dir <- paste(dir,'/',sep='')
formatted_file <- FormatMCLFastas(dir)
# }