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lib/Bio/Polloc/Rule/repeat.pm  view on Meta::CPAN

=head2 stringify_value

Produces a readable string containing the value of the rule.

=cut

sub stringify_value {
   my ($self,@args) = @_;
   my $out = "";
   for my $k (keys %{$self->value}){
      $out.= "$k=>".(defined $self->value->{$k} ? $self->value->{$k} : "")." ";
   }
   return $out;
}

=head2 value

Implements the C<_qualify_value()> from the L<Bio::Polloc::RuleI> interface

=head3 Arguments

Value (str or ref-to-hash or ref-to-array).  The supported keys are:

=over

=item -res I<float>

Resolution (allowed error)

=item -minsize I<int>

Minimum size of the repeat

=item -maxsize I<int>

Maximum size of the repeat

=item -minperiod I<float>

Minimum period of the repeat

=item -maxperiod I<float>

Maximum period of the repeat

=item -exp I<float>

Minimum exponent (number of repeats)

=item -allowsmall I<bool (int)>

If true, allows spurious results

=item -win I<float>

Process by sliding windows of size C<2*n> overlaping by C<n>

=item -minsim I<float>

Minimum similarity percent

=item -maxsim I<float>

Maximum similarity percent

=back

=head3 Return

Value (I<hashref> or C<undef>).

=head1 INTERNAL METHODS

Methods intended to be used only within the scope of Bio::Polloc::*

=head2 _calculate_consensus

Attempts to calculate the consensus of the repeat units.

=head3 Arguments

The repetitive sequence with repeat units separated by spaces (I<str>).

=head3 Returns

The consensus sequence (I<str>)

=cut

sub _calculate_consensus {
   my($self,$seq) = @_;
   return unless $seq;
   my $io = Bio::Polloc::Polloc::IO->new();
   my $emma = $io->exists_exe("emma");
   my $cons = $io->exists_exe("cons");
   return "no-emma" unless $emma;
   return "no-cons" unless $cons;
   my ($outseq_fh, $outseq) = $io->tempfile;
   my $i=0;
   print $outseq_fh ">".(++$i)."\n$_\n" for split /\s+/, $seq;
   close $outseq_fh;
   return "err-seq" unless -s $outseq;
   my $outaln = "$outseq.aln";
   my $emmarun = Bio::Polloc::Polloc::IO->new(-file=>"$emma '$outseq' '$outaln' '/dev/null' -auto >/dev/null |");
   while($emmarun->_readline){ print STDERR $_ }
   $emmarun->close();
   unless(-s $outaln){
      unlink $outaln if -e $outaln;
      return "err-aln";
   }
   my $consout = "";
   my $consrun = Bio::Polloc::Polloc::IO->new(-file=>"$cons '$outaln' stdout -auto |");
   while(my $ln = $consrun->_readline){
      chomp $ln;
      next if $ln =~ /^>/;
      $consout .= $ln;
   }
   unlink $outaln;
   $consrun->close();
   $io->close();
   return $consout;
}

=head2 _parameters