mapAcc2Name

Default renameFA() replacement function. Maps an accession number to its name

Default rename_fasta() replacement function. Maps an accession number to its name

Usage

mapAcc2Name(line, acc2name, acc_col = "AccNum", name_col = "Name")

mapAcc2Name(line, acc2name, acc_col = "AccNum", name_col = "Name")

Arguments

line

The line of a fasta file starting with '>'

acc2name

Data Table containing a column of accession numbers and a name column

acc_col

Name of the column containing Accession numbers

name_col

Name of the column containing the names that the accession numbers are mapped to

Value

A character string representing the updated FASTA line, where the accession number is replaced with its corresponding name.

Character string. The modified line from the Fasta file header with the name instead of the accession number.

Examples

if (FALSE) { # \dontrun{
mapAcc2Name(">P12345 some description", acc2name, "AccNum", "Name")
} # }
if (FALSE) { # \dontrun{
acc2name_table <- data.table(AccNum = c("ACC001", "ACC002"),
Name = c("Species A", "Species B"))
line <- ">ACC001 some additional info"
mapped_line <- mapAcc2Name(line, acc2name_table)
mapped_line  # Expected output: ">Species A"
} # }