convert BED file to FASTA (one per cluster)

bin/bed_to_fasta.R

@@ -0,0 +1,25 @@
+bed <- data.table::data.table(1:10,1:10,c("AAAAAAAAA","CTGAGA","CCCTAGC","GC","AA","ACGTACGTGTCA","GGGCCGCTA","GCA","TTTTTGCA","AAAATCGACGT"),c(1,2,3,1,1,1,2,2,3,3))
+
+#!/usr/bin/env Rscript
+
+# Splitting BED-files depending on their cluster.
+# The Sequences of each cluster are writen as an FASTA-file.
+# @parameter bedInput <string> BED-file with sequences and cluster-id as column
+# @parameter out <string> output directory
+# @parameter prefix <string> prefix for filenames
+
+args = commandArgs(trailingOnly = TRUE)
+
+
+bedInput <- args[1]
+out <- args[2] # "G://Rene.Wiegandt/10_Master/"
+prefix <- args[3] # "Fasta" 
+
+bed <- data.table::fread(bedInput, header = FALSE, sep = "\t")
+
+clusters <- split(bed, bed$V4, sorted = TRUE, flatten = FALSE) # <---- Spalte mit Cluster
+discard <- lapply(1:length(clusters), function(i){
+  sequences <- as.list(as.data.frame(clusters[i])[[3]])   # <---- Splate mit Sequenz
+  outfile <- paste0(out,prefix,"_cluster_",i)
+  seqinr::write.fasta(sequences = sequences, names = as.data.frame(clusters[i])[[2]], file.out = outfile, as.string = TRUE) # <---- Spalte mit Name
+})