#!/usr/bin/perl -w

use strict;

open(OUTFILE1, ">Pim173ArrayWithNames.txt");
open(OUTFILE2, ">Pim173NumberedMSA.txt");

my @names = ();
my $i = 0;

{
  local $/ = "\n>";
  
  while(my $entry = <>)
  {
    $i = $i+1;
    
    $entry =~ s/^>|>\s*$//g;
    
    my ($title, $sequence) = split(/[\n\r]+/, $entry, 2);
    
    $title =~ /^(.*)/;   
    
    push(@names,$1);
    
    print OUTFILE2 ">q$i\n$sequence\n"
   }
}

print OUTFILE1 join("\n", @names), "\n";

print "Number of sequences renamed: $i\n";
close(OUTFILE1);
close(OUTFILE2);