Bio::Tools::Prepeat - Finding repeats in protein sequences

    use Bio::Tools::Prepeat;
    my $p = Bio::Tools::Prepeat->new( wd => './working_directory' );
    $p->feed(@seq);
    $p->buildidx();
    $result = $p->query();

  my $p = Bio::Tools::Prepeat->new( wd => './working_directory' );

  $p->feed($seq1, $seq2);

  $p->reset();

  $p->buildidx();

  $p->loadidx();

    $p->query(10);

    $p->query([4..10]);

   $p->random_sequence(100000);

    use Bio::Tools::Prepeat qw(random_sequence);
    print random_sequence(100000);

package Bio::Tools::Prepeat;
use 5.006;
use strict;
our $VERSION = '0.06';
use XSLoader;
XSLoader::load 'Bio::Tools::Prepeat';
use Exporter;
our @ISA = qw(Exporter);
our @EXPORT_OK = qw(random_sequence);
use Cwd qw(abs_path);
use String::Random qw(random_string);
use IO::File;

use Data::Dumper;

our @amino = qw/A C D E F G H I K L M N P Q R S T V W Y/;
our @extamino = 'A'..'Z'; # extended amino acid
sub random_sequence { ref($_[0]) ? shift : undef;random_string('0'x(shift), \@amino) }

sub new {
    my $pkg = shift;
    my $arg = ref($_[0]) ? $_[0] : {@_};
    die "It exists as a non-directory\n" if -e $arg->{wd} && !-d $arg->{wd};
    mkdir abs_path($arg->{wd});
    bless {
	wd => abs_path($arg->{wd}),
	seqarr => undef,
    }, $pkg;
}

sub reset {
    my $pkg = shift;
    @{$pkg->{seqarr}} = ();
    @{$pkg->{acclen}} = ();
    $pkg->{built} = 0;
}

sub feed { push @{(shift)->{seqarr}}, map{uc$_}@_ }

# cartesian product over @extamino X @extamino
sub bigram_set {
    my @ret;
    foreach my $f (@extamino){
	foreach my $s (@extamino){
	    push @ret, $f.$s;
	}
    }
    @ret;
}

sub loadseq {
    my $pkg = shift;
    open F, $pkg->{wd}."/seqs" or die "Cannot load sequence file\n";
    while(chomp($_=<F>)){
	push @{$pkg->{seqarr}}, $_;
    }
    close F;
}

# accumulating lengths
sub acclen {
    my $pkg = shift;
    my $sum;
    push @{$pkg->{acclen}}, 0;
    for (1..$#{$pkg->{seqarr}}){
	$sum += length $pkg->{seqarr}->[$_-1];
	push @{$pkg->{acclen}}, $sum;
    }
}

sub loadidx {
    my $pkg = shift;
    $pkg->{seqarr} = $pkg->{acclen} = undef;
    $pkg->loadseq;
    $pkg->acclen;
    $pkg->{built} = 1;
}

sub buildidx {
    my $pkg = shift;
    my %fh;

    $pkg->acclen;

    foreach (bigram_set){
	$fh{$_} = new IO::File $pkg->{wd}."/idx.$_", O_CREAT|O_WRONLY|O_TRUNC;
	die "Cannot open index file $_ for writing\n" unless defined $fh{$_};
    }

    open F, '>', $pkg->{wd}."/seqs";
    my $cnt = 0;
    foreach my $seq (@{$pkg->{seqarr}}){
	print F "$seq\n";
	for(my $i = 0; $i < length($seq)-1; $i++){
	    my $bigram = substr($seq, $i, 2);
	    my $h = $fh{$bigram};
	    print $h ($pkg->{acclen}->[$cnt] + $i)."\n";
	}
	$cnt++;
    }
    close F;

    $_->close foreach (values %fh);
    $pkg->{built} = 1;
}

# relative position
sub relpos {
    my ($pkg, $abspos) = @_;
    my ($seqid, $pos) = (0, 0);
    for( my $i=$#{$pkg->{acclen}} ; $i>=0 ; $i--){
	if( $abspos >= $pkg->{acclen}->[$i] ){
	    $pos = $abspos - $pkg->{acclen}->[$i];
	    $seqid = $i;
	    last;
	}
    }
    return ($seqid, $pos);
}

# absolute position
sub abspos {
    my ($pkg, $seqid, $pos) = @_;
    return $pkg->{acclen}->[$seqid] + $pos;
}

sub coincidence_length {
    my ($pkg, $prev, $this) = @_;
    my @prevrel = $pkg->relpos($prev);
    my @thisrel = $pkg->relpos($this);
    my @range = @{$pkg->{length}};
    my @ret;

    foreach my $len (@range){
	my $str_a = substr($pkg->{seqarr}->[$prevrel[0]], $prevrel[1], $len);
	my $str_b = substr($pkg->{seqarr}->[$thisrel[0]], $thisrel[1], $len);
#	print "$len $str_a $str_b$/" if $str_a =~/^ACL/o || $str_b =~ /^ACL/o;

	last if length $str_a != $len || length $str_b != $len;
	last if $str_a ne $str_b;
#    print "$prev, $this => ", substr($pkg->{seqarr}->[$prevrel[0]], $prevrel[1], $pkg->{length}), '/', substr($pkg->{seqarr}->[$thisrel[0]], $thisrel[1], $pkg->{length}), $/;
	push @ret, [ \@prevrel, \@thisrel, $len ];
    }
    \@ret;
}

use List::Util qw/min/;
sub query {
    my ($pkg, $length) = @_;
    die "Index files are not built or loaded. Please use 'buildidx' or 'loadidx' first\n" unless $pkg->{built};
    die "Length of a repeat sequence must exceed 3\n" unless $length >= 3;
    $pkg->{length} = ref($length) ? [sort{$a<=>$b}@$length] : [ $length ];
    open R, '>', $pkg->{wd}."/result";
    my ($prev, $this);
    foreach (bigram_set){
	next unless -s $pkg->{wd}."/idx.$_";
	open F, $pkg->{wd}."/idx.$_" or die "Cannot open index file $_ for query\n";
	my @posarr;
	while ( chomp ($_ = <F>) ){ push @posarr, $_; }

	my %checked;
	foreach $prev (@posarr){
	    next if $checked{$prev};
	    foreach $this (@posarr){
		if($this - $prev > min( @{$pkg->{length}})){
		    my $occs = $pkg->coincidence_length($prev, $this);
		    if(ref $occs){
			foreach my $occ (@{$occs}){
			    $checked{$pkg->abspos($occ->[0]->[0], $occ->[0]->[1])} = 1;
#			    print substr($pkg->{seqarr}->[$occ->[0]->[0]],$occ->[0]->[1], $occ->[2]),$/;

			    print R
				join ' ',
				substr($pkg->{seqarr}->[$occ->[0]->[0]],
				       $occ->[0]->[1], $occ->[2]),
				"@{$occ->[0]} @{$occ->[1]}\n";
			}
		    }
		}
	    }
	}
	close F;
    }
    close R;

    open R, $pkg->{wd}."/result" or die "Cannot open result file\n";
    my $ret;
    while(chomp($_=<R>)){
	my @e = split /\s/, $_;
	$ret->{$e[0]}->{join q/ /,@e[1..2]} = 1;
	$ret->{$e[0]}->{join q/ /,@e[3..4]} = 1;
    }
    close R;
    foreach (keys %{$ret}){
	$ret->{$_} = [ 
		       sort{ $a->[0] <=> $b->[0] }
		       sort{ $a->[1] <=> $b->[1] }
		       map { [split/ /] }
		       keys %{$ret->{$_}}
		       ];
    }
    $ret;
}


sub cleanidx {
    map{unlink $_} glob($_[0]->{wd}."/*");
    rmdir $_[0]->{wd};
}



1;
__END__
# Below is stub documentation for your module. You better edit it!