mariokostelac · September 4, 2015 14:23
diff --git a/extract_reads.sh b/extract_reads.sh
 #!/usr/bin/env bash

 output_dir=${1-.}

 DONE=false
 i=0
 until $DONE; do
  read header || DONE=true
  read seq || DONE=true
  echo $header > $output_dir/$i.fasta
  echo $seq >> $output_dir/$i.fasta
  i=$(($i+1))
 done;
	#!/usr/bin/env bash

	output_dir=${1-.}

	DONE=false
	i=0
	until $DONE; do
	read header \|\| DONE=true
	read seq \|\| DONE=true
	echo $header > $output_dir/$i.fasta
	echo $seq >> $output_dir/$i.fasta
	i=$(($i+1))
	done;