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

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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)

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