FormatMCLFastas: Format all raw GenBank fastas to single OrthoMCL compatible...
In corinsexton/MAGNAMWAR: A Pipeline for Meta-Genome Wide Association
Description
Usage
Arguments
Value
Examples
Description
Creates the composite fasta file for use in running OrthoMCL and/or submitting to www.orthomcl.org
Usage
1
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
1
2
3
dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
dir <- paste(dir,'/',sep='')
formatted_file <- FormatMCLFastas(dir)
corinsexton/MAGNAMWAR documentation built on May 13, 2019, 10:51 p.m.
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Description Usage Arguments Value Examples
Description
Creates the composite fasta file for use in running OrthoMCL and/or submitting to www.orthomcl.org
Usage
1 | 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
1 2 3 | dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
dir <- paste(dir,'/',sep='')
formatted_file <- FormatMCLFastas(dir)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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