#!/usr/local/bin/perl
#use strict; 
use warnings;
use Errno;
use lib " /RemotePerl";
use lib " /System/Library/Perl/5.8.6";
use lib " /Library/Perl/5.8.6";
use Bio::Perl;
use Bio::SeqIO;
use IO::String;
use Bio::SearchIO;

if (@ARGV < 2) { die "usage: compare.pl <filename1> <filename2>\n"; }

$file1 = $ARGV[0];
$file2 = $ARGV[1];

#Read in first fasta file
$FastaFile1 = Bio::SeqIO->new(-file => $ARGV[0], -format => 'fasta');
print "File name of the first fasta file is: ".$file1."\n";

#Create array of the fasta sequences from file 1
my @fasta_objs =();

#Add sequences of file1 to array called fasta_objs
while (my $seqFile1 = $FastaFile1->next_seq() )
{
push @fasta_objs,$seqFile1->seq;
}

#Read in second fasta file
$FastaFile2 = Bio::SeqIO->new(-file => $ARGV[1], -format => 'fasta');
print "File name of the first fasta file is: ".$file2."\n";

#Setup output file: sequences from File2 which match sequences of File1
my $fasta = Bio::SeqIO->new(-file => ">EQUAL_HITS.fasta", -format => "fasta", -flush  => 0);

# write matching sequences of file2 to the output file
# Note that if several matches to one sequence exist, ALL matches are output to the file
while(my $seqFile2 = $FastaFile2->next_seq() )
{
        $fasta->write_seq($seqFile2) if (grep {$_ eq $seqFile2->seq} @fasta_objs);
}

print "Comparison is complete! \n";