#!/usr/bin/perl -w
use strict;
open(my $in,"/Users/Desktop/Pipelines/fungi.1.aa.hypothetical.faa");
open(my $out,">Users/Desktop/Pipelines/fungi.1.aa.hypothetical50.faa"); 

local $/ = undef;
my @chunks = split(/>/, <$in>);
my @hypothetical50 = @chunks[0..49];
for my $hypothetical50(@hypothetical50){
	if($hypothetical50 =~ s/^gi/>gi/g){
		print $out "$hypothetical50\n";
	}
} 
close($in);
close($out);