generateAllAlignments2FA

Adding Leaves to an alignment file w/ accessions

Adding Leaves to all alignment files w/ accessions & DAs?

Usage

generateAllAlignments2FA(
  aln_path = here("data/rawdata_aln/"),
  fa_outpath = here("data/alns/"),
  lin_file = here("data/rawdata_tsv/all_semiclean.txt"),
  reduced = FALSE
)

Arguments

aln_path

Character. Path to alignment files. Default is 'here("data/rawdata_aln/")'

fa_outpath

Character. Path to file. Master protein file with AccNum & lineages. Default is 'here("data/rawdata_tsv/all_semiclean.txt")'

lin_file

Character. Path to the written fasta file. Default is 'here("data/alns/")'.

reduced

Boolean. If TRUE, the fasta file will contain only one sequence per lineage. Default is 'FALSE'.

Value

NULL. The function saves the output FASTA files to the specified directory.

Details

The alignment files would need two columns separated by spaces:

1. AccNum and 2. alignment. The protein homolog file should have AccNum, Species, Lineages.

Note

Please refer to the source code if you have alternate + file formats and/or column names.

Examples

if (FALSE) { # \dontrun{
generateAllAlignments2FA()
} # }