Translate coding sequences into amino acid sequences — translate_cds_to

A helper function that takes a fasta file storing coding sequences as input and translates these coding sequences into amino acid sequences storing them as fasta output file.

Usage

translate_cds_to_protein(input_file, output_file, delete_corrupt_cds = FALSE)

Arguments

input_file: file path to fasta file storing coding sequences (DNA).
output_file: name or file path in which translated amino acid sequences (AA) shall be stored as fasta file.
delete_corrupt_cds: delete_corrupt_cds a logical value indicating whether sequences with corrupt base triplets should be removed from the input file. This is the case when the length of coding sequences cannot be divided by 3 and thus the coding sequence contains at least one corrupt base triplet.

Author

Hajk-Georg Drost

Examples

if (FALSE) { # \dontrun{
# install.packages("biomartr")
# download coding sequences of Arabidopsis thaliana
Ath_file_path <- biomartr::getCDS(db = "refseq",
                     organism = "Arabidopsis thaliana",
                     gunzip = TRUE)
# translate coding sequences into amino acid sequences
translate_cds_to_protein(Ath_file_path, "Ath_aa_seqs.fasta")
} # }