addLeaves2Alignment

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

Usage

addLeaves2Alignment(
  aln_file = "",
  lin_file = "data/rawdata_tsv/all_semiclean.txt",
  reduced = FALSE,
  seq_type = c("AA", "DNA")
)

Arguments

aln_file

haracter. 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'

reduced

Boolean. If TRUE, a reduced data frame will be generated with only one sequence per lineage. Default is FALSE.

seq_type

Character. Type of sequence, either "AA" or "DNA". Default is "AA".

Value

A data frame containing the enriched alignment data with lineage information.

Details

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.

Author

Janani Ravi

Examples

if (FALSE) { # \dontrun{
addLeaves2Alignment("pspa_snf7.aln", "pspa.txt")
} # }