converts protein accession numbers to a fasta format. Resulting fasta file is written to the outpath.
converts protein accession numbers to a fasta format. Resulting fasta file is written to the outpath.
acc2FA converts protein accession numbers to a fasta format. Resulting fasta file is written to the outpath.
Usage
acc2FA(accessions, outpath, plan = "sequential")
acc2FA(accessions, outpath, plan = "sequential")Arguments
- accessions
Character vector containing protein accession numbers to generate fasta sequences for. Function may not work for vectors of length > 10,000
- outpath
str. Location where fasta file should be written to.
- plan
Character. The plan to use for processing. Default is "sequential".
Value
A logical value indicating whether the retrieval and conversion were
successful. Returns TRUE if successful and FALSE otherwise.
A Fasta file is written to the specified outpath.
Examples
if (FALSE) { # \dontrun{
acc2FA(accessions = c("ACU53894.1", "APJ14606.1", "ABK37082.1"),
outpath = "my_proteins.fasta")
Entrez:accessions <- rep("ANY95992.1", 201) |> acc2FA(outpath = "entrez.fa")
EBI:accessions <- c("P12345", "Q9UHC1",
"O15530", "Q14624", "P0DTD1") |> acc2FA(outpath = "ebi.fa")
} # }
if (FALSE) { # \dontrun{
acc2FA(accessions = c("ACU53894.1", "APJ14606.1", "ABK37082.1"),
outpath = "my_proteins.fasta")
Entrez:accessions <- rep("ANY95992.1", 201) |> acc2FA(outpath = "entrez.fa")
EBI:accessions <- c("P12345", "Q9UHC1", "O15530", "Q14624", "P0DTD1") |>
acc2FA(outpath = "ebi.fa")
} # }