Adding Leaves to an alignment file w/ accessions

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

Usage

convert_aln2fa(
  aln_file = "",
  lin_file = "data/rawdata_tsv/all_semiclean.txt",
  fa_outpath = "",
  reduced = FALSE
)

convert_aln2fa(
  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'

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")
} # }