Adding Leaves to an alignment file w/ accessions

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

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

Usage

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

add_leaves(
  aln_file = "",
  lin_file = "data/rawdata_tsv/all_semiclean.txt",
  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'

reduced

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

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