R/faRemoveChrom.R

In dvera/travis: R Utilities for Bed and BEdgRaphs

faRemoveChrom <- function( fastaFiles , removePatterns , suffix="_rmChr", threads=getOption("threads",1L) ){

  
  outnames<-paste0(basename(removeext(fastaFiles)),suffix,".fa")
	searchString <- paste0(paste0("$1 ~ /",removePatterns),"/",collapse=" || ")
  cmdString <- paste("awk '{if($1~/^>/){if(",searchString,"){a=0}else{a=1}};if(a==1){print $0}}'",fastaFiles,">",outnames)
  res <- cmdRun(cmdString, threads=threads)
  return(outnames)
  
}