Raw content of BioMart::Formatter::TSV # $Id: TSV.pm,v 1.3 2007/01/09 17:16:00 rh4 Exp $ # # BioMart module for BioMart::Formatter::TSV # # You may distribute this module under the same terms as perl # itself. # POD documentation - main docs before the code. =head1 NAME BioMart::Formatter::TSV =head1 SYNOPSIS The TSV Formatter returns tab separated tabular data for a BioMart query's ResultTable =head1 DESCRIPTION When given a BioMart::ResultTable containing the results of a BioMart::Query the 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 =head1 AUTHORS =over =item * Damian Smedley =back =head1 CONTACT 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 =head1 METHODS =cut package BioMart::Formatter::TSV; use strict; use warnings; # Extends BioMart::FormatterI use base qw(BioMart::FormatterI); use Readonly; # Constants Readonly my $FIELD_DELIMITER => qq{\t}; Readonly my $RECORD_DELIMITER => qq{\n}; sub _new { my ($self) = @_; $self->SUPER::_new(); } sub processQuery { my ($self, $query) = @_; $self->set('original_attributes',[@{$query->getAllAttributes()}]) if ($query->getAllAttributes()); $self->set('query',$query); return $query; } sub nextRow { my $self = shift; my $rtable = $self->get('result_table'); my $row = $rtable->nextRow; if (!$row){ return; } # Escape delimiters in value-strings foreach(@{$row}) { $_ = q{} unless defined ($_); $_ =~ s/$FIELD_DELIMITER/\$FIELD_DELIMITER/g; } # Create the final record-string return join($FIELD_DELIMITER, @{$row}) . $RECORD_DELIMITER; } sub getDisplayNames { my $self = shift; my @displayNames = $self->getTextDisplayNames(); # Enclose non-numeric values in double quotes & escape the quotes already in them map { s/$FIELD_DELIMITER/\$FIELD_DELIMITER/g } @displayNames; # Create the final header string return join($FIELD_DELIMITER, @displayNames) . $RECORD_DELIMITER; } 1;