Perl script for extracting hypothetical proteins from a multi-protein file. The input file must be in single-line fasta format.

Extract_hypothetical_proteins.pl

#!/usr/bin/perl -w
#Executng the program requires sequence.fasta as single line fasta file
open(FH,"sequence.fasta") or die "file doesn't exist"; #sequence.fasta is the input file
open(OT,">>hypothetical_proteins.fasta");
@ff = <FH>;
$t="";
for($i=0;$i<@ff;$i++){
	if($ff[$i]=~m/hypothetical/){
		$t.= $ff[$i].$ff[$i+1];
	}
}
print OT $t;