Renaming all the sequences in a FASTA file automatically
Published:
I came across the problem of renaming sequences in a FASTA sequence alignment after downloading over 200 sequences from GenBank for four different genes. The sequence names were assigned by the GenBank accession number (e.g. MK1526) only. I wanted the sequence names to have the species name in it as well, for example MK1526_Canis_lupis. To avoid the tedious task of manually doing this, I wrote a few lines of R code that I hope will be of use to others with the same issue.
One first needs an Excel .csv file with a column of species/taxon names, and a column with the associated GenBank ID. For example:
| taxon_name | country | genbank |
|---|---|---|
| Ectrosia schultzii Benth. | Australia | MK872740 |
| Cladoraphis spinosa (L.f.) S.M.Phillips | South Africa | GU360600 |
| Ectrosia lasioclada (Merr.) S.T.Blake | Australia | MK872659 |
The aim is to generate the third column (“name”) shown below:
| Taxon name | Country | GenBank | name |
|---|---|---|---|
| Ectrosia schultzii Benth. | Australia | MK872740 | MK872740_Ectrosia_schultzii |
| Cladoraphis spinosa (L.f.) S.M.Phillips | South Africa | GU360600 | GU360600_Cladoraphis_spinosa |
| Ectrosia lasioclada (Merr.) S.T.Blake | Australia | MK872659 | MK872659_Ectrosia_lasioclada |
And then use that column to rename the sequences.
# set your working directory to your desired folder location
# read the csv file
taxa_rps16trnk = read.csv("rps16trnk.csv")
library(stringr)
# change the first column so that it only contains the first two words (genus and species, separated by a space)
taxa_rps16trnk$taxon_name = stringr::word(taxa_rps16trnk$taxon_name, 1,2, sep=" ")
# remove any cases of new line characters
taxa_rps16trnk$taxon_name = str_replace_all(taxa_rps16trnk$taxon_name, "[\r\n]" , "")
# remove any characters from a round bracket onwards, in case there isn't a space between the species name and the bracket
taxa_rps16trnk$taxon_name = gsub("[(].*","", taxa_rps16trnk$taxon_name)
# add an underscore between the genus and species name
taxa_rps16trnk$taxon_name = gsub(" ", "_", taxa_rps16trnk$taxon_name)
# paste the GenBank number and genus_species name together into a new column
taxa_rps16trnk$name = paste(taxa_rps16trnk$rps16.trnK, taxa_rps16trnk$taxon_name)
# replace the space between them with an underscore
taxa_rps16trnk$name <- gsub(" ", "_", taxa_rps16trnk$name)
# optionally write this as a csv file to your working directory
write.csv(taxa_rps16trnk, "rps16trnk.csv")
# create a vector of the new names
new = taxa_rps16trnk$name
current = ape::read.FASTA("rps16trnk.fas")
# create a dataframe with two columns: one with the current sequence names directly from the FASTA file, and one with the new names you want to change them to
ref = data.frame(matrix(nrow = length(new), ncol = 2))
ref[,1] = names(current)
ref[,2] = new
# use the phylotools library to replace the names
library(phylotools)
rename.fasta(infile = "rps16trnk.fas", ref, outfile = "renamed_rps16trnk.fasta")
