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Summary

BioMart::Formatter::DIFF_TSV

Package variables

Included modules

Inherit

BioMart::FormatterI

Synopsis

The DIFF_TSV Formatter returns tab separated tabular data
for a BioMart query's ResultTable

Description

When given a BioMart::ResultTable containing the results of
a BioMart::Query the DIFF_TSV Formatter will return tabular output
with one line for each row of data in the ResultTable and tabs
separating the individual entries in each row. The getDisplayNames
and getFooterText can be used to return appropiately formatted
headers and footers respectively

Methods

Methods description

None available.

Methods code

sub _new {

    my ($self) = @_;

    $self->SUPER::_new();
    $self->attr('reference',0);

}

sub getDisplayNames {

    my $self = shift;
    my @displayNames = $self->getTextDisplayNames();

    if ($self->get('reference')){
        $displayNames[-1] .= " (Reference)";
    }


    # Enclose non-numeric values in double quotes & escape the quotes already in them
    map { s/$FIELD_DELIMITER/\$FIELD_DELIMITER/g } @displayNames;
    
    # Create the final header string
    return join($FIELD_DELIMITER, @displayNames) . $RECORD_DELIMITER;
}

1;

}

sub getFormatterDisplayName {

    return 'Diff to reference (tab separated)';

}

sub nextRow {

    my $self = shift;

    my $rtable = $self->get('result_table');
    my $row = $rtable->nextRow;
    if (!$row){
        return;
    }

    my $reference;
    if ($self->get('reference')){
	$reference= $$row[-1];

	if (!$reference){
	    return "\n";
	}
    }
    my $result_seen;


    # Escape delimiters in value-strings
    for (my $i = 0; $i < @{$row}; $i++) {


	if (($i != @{$row} - 1) && ($$row[$i] eq $reference) && $$row[$i] && $reference){
	    $$row[$i] = '';
        }


	if ($reference){
	    $result_seen = 1 if ($$row[$i] =~ /^[ACGT]$/ && ($i != @{$row} - 1));
	}
	else{
	    $result_seen = 1 if ($$row[$i] =~ /^[ACGT]$/ );
	}


	$$row[$i] = q{} unless defined ($$row[$i]);
	$$row[$i] =~ s/$FIELD_DELIMITER/\$FIELD_DELIMITER/g;
    }
    if ($result_seen){
	# Create the final record-string
	return join($FIELD_DELIMITER, @{$row}) . $RECORD_DELIMITER;
    }
    else{
	return "\n";
    }

}

sub processQuery {

    my ($self, $query) = @_;

    my $filters = $query->getAllFilters();
    my @filts;
    foreach my $filter(@{$filters}){
        if ($filter->name eq 'reference_strain'){
            my $rows = $filter->get('attribute_table')->getRows();
            my $ref_strain = ${$$rows[0]}[0];
            # remove the filter

	$ref_strain =~ s/\//\_/g;
	$ref_strain =~ s/ /\_/g;
	$ref_strain =~ s/\+/\_/g;
	$ref_strain =~ s/\./\_/g;
	$ref_strain =~ s/\-/\_/g;
	$query->addAttribute(lc($ref_strain));
	$self->set('reference',1);
    }
    else{
	push @filts,$filter;
    }
}
$query->removeAllFilters();
$query->addFilters(\@filts);


    $self->set('original_attributes',[@{$query->getAllAttributes()}]) 
	if ($query->getAllAttributes());
    $self->set('query',$query);
    return $query;

}

General documentation

This module is part of the BioMart project
http://www.biomart.org
Questions can be posted to the mart-dev mailing list: mart-dev@ebi.ac.uk