Bio-ToolBox

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MANIFEST  view on Meta::CPAN

lib/Bio/ToolBox.pm
lib/Bio/ToolBox/big_helper.pm
lib/Bio/ToolBox/Data.pm
lib/Bio/ToolBox/Data/core.pm
lib/Bio/ToolBox/Data/file.pm
lib/Bio/ToolBox/Data/Feature.pm
lib/Bio/ToolBox/Data/Iterator.pm
lib/Bio/ToolBox/Data/Stream.pm
lib/Bio/ToolBox/GeneTools.pm
lib/Bio/ToolBox/db_helper.pm
lib/Bio/ToolBox/db_helper/alignment_callbacks.pm
lib/Bio/ToolBox/db_helper/bam.pm
lib/Bio/ToolBox/db_helper/bigbed.pm
lib/Bio/ToolBox/db_helper/big.pm
lib/Bio/ToolBox/db_helper/bigwig.pm
lib/Bio/ToolBox/db_helper/constants.pm
lib/Bio/ToolBox/db_helper/config.pm
lib/Bio/ToolBox/db_helper/hts.pm
lib/Bio/ToolBox/db_helper/seqfasta.pm
lib/Bio/ToolBox/db_helper/useq.pm
lib/Bio/ToolBox/db_helper/wiggle.pm

META.json  view on Meta::CPAN

         "version" : "2.00"
      },
      "Bio::ToolBox::big_helper" : {
         "file" : "lib/Bio/ToolBox/big_helper.pm",
         "version" : "2.00"
      },
      "Bio::ToolBox::db_helper" : {
         "file" : "lib/Bio/ToolBox/db_helper.pm",
         "version" : "2.00"
      },
      "Bio::ToolBox::db_helper::alignment_callbacks" : {
         "file" : "lib/Bio/ToolBox/db_helper/alignment_callbacks.pm",
         "version" : "2.00"
      },
      "Bio::ToolBox::db_helper::bam" : {
         "file" : "lib/Bio/ToolBox/db_helper/bam.pm",
         "version" : "2.00"
      },
      "Bio::ToolBox::db_helper::big" : {
         "file" : "lib/Bio/ToolBox/db_helper/big.pm",
         "version" : "2.00"
      },

META.yml  view on Meta::CPAN

    version: '2.00'
  Bio::ToolBox::SeqFeature:
    file: lib/Bio/ToolBox/SeqFeature.pm
    version: '2.00'
  Bio::ToolBox::big_helper:
    file: lib/Bio/ToolBox/big_helper.pm
    version: '2.00'
  Bio::ToolBox::db_helper:
    file: lib/Bio/ToolBox/db_helper.pm
    version: '2.00'
  Bio::ToolBox::db_helper::alignment_callbacks:
    file: lib/Bio/ToolBox/db_helper/alignment_callbacks.pm
    version: '2.00'
  Bio::ToolBox::db_helper::bam:
    file: lib/Bio/ToolBox/db_helper/bam.pm
    version: '2.00'
  Bio::ToolBox::db_helper::big:
    file: lib/Bio/ToolBox/db_helper/big.pm
    version: '2.00'
  Bio::ToolBox::db_helper::big::BedIteratorWrapper:
    file: lib/Bio/ToolBox/db_helper/big.pm
  Bio::ToolBox::db_helper::big::BigWigSet:

lib/Bio/ToolBox/db_helper/alignment_callbacks.pm  view on Meta::CPAN

package Bio::ToolBox::db_helper::alignment_callbacks;

use warnings;
use strict;
use Carp;
use Bio::ToolBox::db_helper::constants;
require Exporter;

our $VERSION = '2.00';

# Exported names

lib/Bio/ToolBox/db_helper/alignment_callbacks.pm  view on Meta::CPAN

	# these subroutines are designed to work with the low level fetch API

	# there are so many different subroutines because I want to increase
	# efficiency by limiting the number of conditional tests in one generic subroutine

	# passed parameters as array ref
	# chromosome, start, stop, strand, strandedness, method, value, db, dataset
	my $param = shift;

	# check the current list of calculated callbacks
	# cache the calculated callback method to speed up subsequent data
	# collections it's likely only one method is ever employed in an
	# execution, but just in case we will cache all that we calculate
	my $string = sprintf "%s_%s_%s_%d", $param->[STND], $param->[STR],
		$param->[METH], $param->[RETT];
	return $CALLBACKS{$string} if exists $CALLBACKS{$string};

	# determine the callback method based on requested criteria
	my $callback;

lib/Bio/ToolBox/db_helper/alignment_callbacks.pm  view on Meta::CPAN

			or ( $e >= $data->{start} and $e <= $data->{stop} ) );
	push @{ $data->{scores} }, $a->qname;
}

1;

__END__

=head1 NAME

Bio::ToolBox::db_helper::alignment_callbacks

=head1 DESCRIPTION

This module provides common callback subroutines for working with bam alignments. 
It is generalized and may be used with either L<Bio::DB::Sam> or L<Bio::DB::HTS> 
adapter objects. 

It's not meant to be used by individuals. 

=head1 SEE ALSO

lib/Bio/ToolBox/db_helper/bam.pm  view on Meta::CPAN

package Bio::ToolBox::db_helper::bam;

use warnings;
use strict;
use Carp;
use File::Copy;
use English qw( -no_match_vars );
use Bio::ToolBox::db_helper::constants;
use Bio::ToolBox::db_helper::alignment_callbacks;
use Bio::DB::Sam;
require Exporter;

my $parallel;
eval {
	# check for parallel support, when counting bam alignments
	require Parallel::ForkManager;
	$parallel = 1;
};

lib/Bio/ToolBox/db_helper/hts.pm  view on Meta::CPAN

package Bio::ToolBox::db_helper::hts;

use warnings;
use strict;
use Carp;
use English qw(-no_match_vars);
use Bio::ToolBox::db_helper::constants;
use Bio::ToolBox::db_helper::alignment_callbacks;
use Bio::DB::HTS;
require Exporter;

my $parallel;
eval {
	# check for parallel support, when counting bam alignments
	require Parallel::ForkManager;
	$parallel = 1;
};