#!/usr/bin/perl

use strict;
use warnings;
use Bio::AlignIO;
use Bio::SimpleAlign;

my $ref = "rCRS.fas";

my $comp = shift @ARGV or die "please provide comparison sequence: $!\n";

my $comp_id;

if ($comp =~ /(\S*)\.fas*/) {
    $comp_id = $1;
}

my $CAT = "cat $ref ".$comp." > ".$comp.".tmp";
try_cmd($CAT);

my $ALN = "muscle -in ".$comp.".tmp -out ".$comp.".aln";
try_cmd($ALN);

my $str = Bio::AlignIO->new(
     -file => $comp.".aln",
    -format => "fasta",
    );

my $aln = $str->next_aln();

####Subroutine####

sub try_cmd {
    my $cmd = shift;
    my $status;
    $status = system($cmd);
    if ( $status ) {
	print STDERR ( "problem running $cmd\nReturned $status
n" );
    }
    else {
	print STDERR ( "Successfully ran $cmd\n" );
    }
}

##</code><code>##


>Ref_seq    AATTTGGGCTACT
>Query_seq  AAATTCGGCTACA

##</code><code>##


3A  6C  12A