convertAlignment2FA

Adding Leaves to an alignment file w/ accessions Genomic Contexts vs Domain Architectures.

Usage

convertAlignment2FA(
  aln_file = "",
  lin_file = "data/rawdata_tsv/all_semiclean.txt",
  fa_outpath = "",
  reduced = FALSE
)

convertAlignment2FA(
  aln_file = "",
  lin_file = "data/rawdata_tsv/all_semiclean.txt",
  fa_outpath = "",
  reduced = FALSE
)

Arguments

aln_file

Character. Path to file. Input tab-delimited file + alignment file accnum & alignment. Default is 'pspa_snf7.aln'

lin_file

Character. Path to file. Protein file with accession + number to lineage mapping. Default is 'pspa.txt'

fa_outpath

Character. Path to the written fasta file. Default is 'NULL'

reduced

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

Value

A character string representing the FASTA formatted sequences. If fa_outpath is provided, the FASTA will also be saved to the specified file.

Character string containing the Fasta formatted sequences. If fa_outpath is specified, the function also writes the sequences to the Fasta file.

Details

The alignment file would need two columns: 1. accession + number and 2. alignment. The protein homolog accession to lineage mapping + file should have

The alignment file would need two columns: 1. accession + number and 2. alignment. The protein homolog accession to lineage mapping + file should have

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{
addLeaves2Alignment("pspa_snf7.aln", "pspa.txt")
} # }

if (FALSE) { # \dontrun{
convertAlignment2FA("pspa_snf7.aln", "pspa.txt")
} # }