generateAllAlignments2FA
Source:R/CHANGED-pre-msa-tree.R
, R/pre-msa-tree.R
generateAllAlignments2FA.Rd
Adding Leaves to an alignment file w/ accessions
Adding Leaves to all alignment files w/ accessions & DAs?
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 = F
)
generateAllAlignments2FA(
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 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.
NULL. The function saves the output FASTA files to the specified directory.
Details
The alignment files would need two columns separated by spaces:
AccNum and 2. alignment. The protein homolog file should have AccNum, Species, Lineages.
The alignment files would need two columns separated by spaces:
AccNum and 2. alignment. The protein homolog file should have AccNum, Species, Lineages.