#!/usr/bin/awk -f

# Tue Oct 21 10:22:36 CEST 2008

# This program receives a file in fasta format and prepares it to be used with RNAfold, i.e. with the whole sequence in a single line

#Use: >./fasta2vienna.awk file


BEGIN{
	RS=">" 		
	FS="\n" 	
}


# Breaks each sequence by newline characters. It prints all 80mers together 



{
	if(NR>=2){	# NR has to start at 2, otherwise it prints useless lines. 
	seq=$0
	split(seq, a, "\n");	
	i=2			
	printf ">%s\n", a[1]
	while(a[i]!=""){	
		printf "%s", a[i]
		i++	
		}	
		printf "%s\n", ""
	}
}