view release on metacpan or  search on metacpan

lib/Bio/ViennaNGS/Peak.pm  view on Meta::CPAN

# -*-CPerl-*-
# Last changed Time-stamp: <2018-07-03 12:20:53 mtw>

package Bio::ViennaNGS::Peak;

use Bio::ViennaNGS;
use Moose;
use Carp;
use Data::Dumper;
use Path::Class;
use List::Util qw(sum sum0 min max first);
use Bio::ViennaNGS::Util qw(sortbed);
use namespace::autoclean;
use File::Temp qw(tempfile);
use version; our $VERSION = version->declare("$Bio::ViennaNGS::VERSION");

has 'data' => (
	       is => 'ro',
	       isa => 'HashRef',
	       predicate => 'has_data',
	       default => sub { {} },
	      );

has 'region' => (
		 is => 'ro',
		 isa => 'HashRef',
		 predicate => 'has_region',
		 default => sub { {} },
		);

has 'peaks' => (
		 is => 'ro',
		 isa => 'HashRef',
		 predicate => 'has_peaks',
		 default => sub { {} },
	       );

has 'winsize' => (
		  is => 'ro',
		  isa => 'Int',
		  predicate => 'has_winsize',
		 );

has 'interval' => (
		   is => 'ro',
		   isa => 'Int',
		   predicate => 'has_interval',
		  );

has 'mincov' => (
		 is => 'ro',
		 isa => 'Int',
		 predicate => 'has_mincov',
		);

has 'length' => (
		 is => 'ro',
		 isa => 'Int',
		 predicate => 'has_length',
		);

has 'threshold' => (
		 is => 'ro',
		 isa => 'Value',
		 predicate => 'has_threshold',
		);

sub populate_data {
  my ($self,$filep,$filen) = @_;
  my $this_function = (caller(0))[3];
  my ($i,$element,$chr,$start,$end,$val,$lastend);
  my $have_lastend = 0;

lib/Bio/ViennaNGS/Peak.pm  view on Meta::CPAN

           whose mean is less than a certain value
           (i.e. C<$self-E<gt>threshold> * peak maximum).

Raw peaks are stored in C<%{$self-E<gt>data}-E<gt>{peaks}>.

Args : C<$dest> contains the output path for results, C<$prefix> the
       prefix used for all output file names. C<$log> is the name of a
       log file, or undef if no logging is reuqired.

Returns : None. The output is a position-sorted BED6 file containing
          all raw peaks.

Notes : It is highly recommended to use I<normalized> input data in
        order to allow for multiple calls of this method with the same
        set of parameters on different samples.

=item final_peaks

Title : final_peaks

Usage : C<$obj-E<gt>final_peaks($dest,$prefix,$log);>

Function : This method characterizes final peaks from RNA-seq coverage
           found in C<%{$self-E<gt>data}-E<gt>{peaks}>. The latter is
           supposed to have been populated by C<$self-E<gt>raw_peaks>.

The procedure for finding final peaks is as follows: For each raw peak
found in C<%{$self-E<gt>data}-E<gt>{peaks}> the window of maximum
coverage is retrieved and a (second) sliding window approach is then
applied to regions both upstream and downstream of the maximum. Peak
boundaries are set at the position where the mean coverage of the
respective window is lower than C<$self-E<gt>threshold> * peak
maximum).

Peaks are reported if their total length (as determined by this
routine) is not longer than C<$self-E<gt>length>.

Args : C<$dest> contains the output path for results, C<$prefix> the
       prefix used for all output file names. C<$log> is the name of a
       log file, or undef if no logging is reuqired.

Returns : None. The output is a position-sorted BED6 file containing
          all candidate peaks.

Notes :

=back

=head1 DEPENDENCIES

=over

=item L<Moose>

=item L<Carp>

=item L<Path::Class>

=item L<List::Util>

=item L<namespace::autoclean>

=back

=head1 SEE ALSO

=over

=item L<Bio::ViennaNGS>

=item L<Bio::ViennaNGS::Util>

=back

=head1 AUTHOR

Michael T. Wolfinger, E<lt>michael@wolfinger.euE<gt>

=head1 COPYRIGHT AND LICENSE

Copyright (C) 2015-2018 by Michael T. Wolfinger

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.10.0 or,
at your option, any later version of Perl 5 you may have available.

This software is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

=cut