i have a csv file with DNA sequences. The file has 4 columns which are the name of the chromosome, the start and end of the sequence and the strand (missing or +). I want to transorme this file in fasta format with Rstudio and with the tool of biostring. But i don't know much about the code whick i have to use. First i download the library of biostring. i use this code: c
sv = read.csv("foo.csv") fa = character(4 * nrow(csv)) fa[c(TRUE, FALSE)] = sprintf("> %s", csv$chr) fa[c(FALSE, TRUE)] = csv$seq writeLines(fa, "foo.fasta")
library(Biostrings) seq = csv$seq names(seq) = csv$id dna = DNAStringSet(seq) write.XStringSet(dna, "foo.fasta").also when i run the code: fa[c(TRUE, FALSE)] = sprintf("> %s", csv$chr), it appears ---Error in fa[c(TRUE, FALSE)] = sprintf("> %s", csv$chr) :replacement has length zero
do you reccomend me some other code? or what should change in this code.
Thank you
1 Answer
If you don't mind not using R to achieve your goal. You can look at bedtools getfasta (documentation) for a command-line solution in Linux.
The usage of is quite simple:
bedtools getfasta -fi yourFasta.fa -bed foo.bed -s-s option for force strandness.
But first you may need to convert your csv foo.csv to a bed format. You can do this in R also:
library(reader)
df <- read_csv("foo.csv")
write_tsv(df, "foo.bed", col_names=FALSE)
