Adding Leaves to an alignment file w/ accessions

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

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

Usage

generate_all_aln2fa(
  aln_path = here("data/rawdata_aln/"),
  fa_outpath = here("data/alns/"),
  lin_file = here("data/rawdata_tsv/all_semiclean.txt"),
  reduced = F
)

generate_all_aln2fa(
  aln_path = here("data/rawdata_aln/"),
  fa_outpath = here("data/alns/"),
  lin_file = here("data/rawdata_tsv/all_semiclean.txt"),
  reduced = F
)

Arguments

aln_path

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

fa_outpath

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

lin_file

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

reduced

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

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.

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.

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

Author

Janani Ravi

Examples

if (FALSE) { # \dontrun{
generate_all_aln2fa()
} # }
if (FALSE) { # \dontrun{
generate_all_aln2fa()
} # }