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
addLeaves2Alignment(
aln_file = "",
lin_file = "data/rawdata_tsv/all_semiclean.txt",
reduced = FALSE
)
addLeaves2Alignment(
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.
Value
A data frame containing the enriched alignment data with lineage information.
A data frame containing the combined alignment and 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
The alignment file would need two columns: 1. accession + number and 2. alignment. The protein homolog accession to lineage mapping + file should have