Bio-ToolBox

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CHANGES  view on Meta::CPAN

	- Improved Big File generation such that Bio::DB::BigWig or
	Bio::DB::BigBed is no longer required just to generate the big file, as
	conversion uses external utilities anyway.
	- Fixed generation of bin values when calculating distribution
	frequencies in scripts data2frequency.pl and graph_histogram.pl

v.1.8.7 (svn 487)
	- Added new command line options to script merge_datasets.pl to control
	the program's behavior. The "--lookupname" option allows you to specify
	the name of the lookup column, while "--manual" turns off all automatic
	guessing of columns. Also improved handling of original_file metadata.
	- Added a new option to collect data from long features (such as genomic
	annotations) instead of point data (microarray or sequence data) in
	script get_relative_data.pl.
	- Added option to convert to and from Roman numerals in chromosome names
	and support for wig files in script change_chr_prefix.pl
	- Added option to change the IP port number when connecting to a remote
	MySQL database host in script get_ensembl_annotation.pl
	- Fixed bug to properly close opened files in script split_data_file.pl
	and avoid unnecessary error messages.
	- Modified statements and warnings regarding step and span values in

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

use List::Util qw(min max sum);
use Bio::ToolBox::db_helper::constants;
use Bio::DB::Big;
require Exporter;

our $VERSION = '2.00';

# Initialize CURL buffers
BEGIN {
	# not clear if this should be done only once or if it's harmless to re-init
	# for every new file, so I guess best to just do it here at the very beginning
	# initialization is only for remote files
	Bio::DB::Big->init();
}

# Exported names
our @ISA = qw(Exporter);

## no critic
## this is never intended to be used directly by end users
## and exporting everything is required

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

	}

	# return collected data
	return wantarray ? %pos2data : \%pos2data;
}

sub sum_total_bigbed_features {

	# there is no easy way to do this with this adapter, except to literally
	# walk through the entire file.
	# well, we do this with bam files, I guess we could do the same here
	# honestly, who uses this????? it's legacy. skip for now until someone complains
	return undef;
}

#### BigWigSet Subroutines

sub open_bigwigset_db {
	my $path = shift;
	return Bio::ToolBox::db_helper::big::BigWigSet->new($path);
}

scripts/pull_features.pl  view on Meta::CPAN

		{

			# report
			printf "  using List column '%s', index $list_index\n",
				$List->name($list_index);
			printf "  using Data column '%s', index $data_index\n",
				$Data->name($data_index);
			return;
		}
		else {
			# nope, do not have a match, forget our guesses
			undef $data_index;
			undef $list_index;
		}

		# try with primary_id column
		$data_index = $Data->id_column;
		$list_index = $List->id_column;

		if ( defined $data_index and defined $list_index ) {

			# report
			printf "  using List column '%s', index $list_index\n",
				$List->name($list_index);
			printf "  using Data column '%s', index $data_index\n",
				$Data->name($data_index);
			return;
		}
		else {
			# nope, do not have a match, forget our guesses
			undef $data_index;
			undef $list_index;
		}
	}

	# check for group number
	if ( $List->number_columns > 1 and not defined $group_index ) {
		my $i = $List->find_column('group');
		if ( defined $i ) {
			$group_index = $i;
		}

		# do we ask for a group or not????? probably not.... keep original functionality
	}
	if ( defined $group_index and not $List->name($group_index) ) {
		die " invalid group index!\n";
	}

	# End automatic guessing of index numbers, ask the user
	unless ( defined $list_index ) {
		$list_index = ask_user_for_index( $List,
			" Enter the unique identifier lookup column index from the List file    "
		);
	}
	unless ( defined $data_index ) {
		$data_index = ask_user_for_index( $Data,
			" Enter the unique identifier lookup column index from the Data file    "
		);
	}