Bio-ToolBox

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CHANGES  view on Meta::CPAN

	  and data2gff.pl.
	- The new_data() method now properly recognizes options in Bio::ToolBox.
	- Added new new_bed() shortcut method to Bio::ToolBox.
	- Avoid writing any metadata or comment lines to TSV files. Presumption
	  is that these are primarily for data export and sharing. Add rudimentary
	  support for writing CSV files.
	- Improve coordinate extraction from coordinate strings, allowing to extract
	  for example from "chr1:123,456-789,000:-".
	- Allow genomic coordinate sorting by coordinate string.
	- Handle new Ensembl gencode tags when filtering in Bio::ToolBox::GeneTools.
	- Implement map quality filtering in low level alignment callbacks used by
	  HTS and Sam adapters. Add new use_minimum_mapq() function in 
	  Bio::ToolBox::db_helper to set the map quality level on global scale.
	- Optimize name counting 'ncount' method in Bio::ToolBox::db_helper.
	- Optimize and update API for counting all alignments in a bam file with
	  sum_total_bam_alignments() functions.
	- Remove outdated functions in manipulate_datasets.pl.
	- Fix bug with setting tag values of zero in SeqFeature objects.
	- Rename splice_data() to split_data() in Bio::ToolBox::Data.

v2.02

MANIFEST  view on Meta::CPAN

CHANGES
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/Feature.pm
lib/Bio/ToolBox/Data/file.pm
lib/Bio/ToolBox/Data/Iterator.pm
lib/Bio/ToolBox/Data/Stream.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/big.pm
lib/Bio/ToolBox/db_helper/bigbed.pm
lib/Bio/ToolBox/db_helper/bigwig.pm
lib/Bio/ToolBox/db_helper/config.pm
lib/Bio/ToolBox/db_helper/constants.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" : "2.03"
      },
      "Bio::ToolBox::big_helper" : {
         "file" : "lib/Bio/ToolBox/big_helper.pm",
         "version" : "2.04"
      },
      "Bio::ToolBox::db_helper" : {
         "file" : "lib/Bio/ToolBox/db_helper.pm",
         "version" : "2.041"
      },
      "Bio::ToolBox::db_helper::alignment_callbacks" : {
         "file" : "lib/Bio/ToolBox/db_helper/alignment_callbacks.pm",
         "version" : "2.03"
      },
      "Bio::ToolBox::db_helper::bam" : {
         "file" : "lib/Bio/ToolBox/db_helper/bam.pm",
         "version" : "2.03"
      },
      "Bio::ToolBox::db_helper::big" : {
         "file" : "lib/Bio/ToolBox/db_helper/big.pm",
         "version" : "2.02"
      },

META.yml  view on Meta::CPAN

    version: '2.00'
  Bio::ToolBox::SeqFeature:
    file: lib/Bio/ToolBox/SeqFeature.pm
    version: '2.03'
  Bio::ToolBox::big_helper:
    file: lib/Bio/ToolBox/big_helper.pm
    version: '2.04'
  Bio::ToolBox::db_helper:
    file: lib/Bio/ToolBox/db_helper.pm
    version: '2.041'
  Bio::ToolBox::db_helper::alignment_callbacks:
    file: lib/Bio/ToolBox/db_helper/alignment_callbacks.pm
    version: '2.03'
  Bio::ToolBox::db_helper::bam:
    file: lib/Bio/ToolBox/db_helper/bam.pm
    version: '2.03'
  Bio::ToolBox::db_helper::big:
    file: lib/Bio/ToolBox/db_helper/big.pm
    version: '2.02'
  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 = '2.03';

# 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. 

=head2 Methods

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;
};