Toolbar

Summary

BioMart::Formatter::TSV_36

Package variables

Included modules

Inherit

BioMart::FormatterI

Synopsis

The TSV_36 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 TSV_36 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();

    # connect to database and get adaptors
    my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
						-HOST     => $host,
						-PORT     => $port,
						-USER     => $user,
						-PASS     => $pass,
						-DBNAME   => $dbname);
    $self->attr('db_adaptor',$db);

}

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;

}

sub getFormatterDisplayName {

    return 'Mouse 36 assembly (TSV)';

}

sub nextRow {

    my $self = shift;

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

    my $chromosome = $$row[-1];
    my $strand = $$row[-2];

    # convert coordinates to NCBI36 assembly
    my @atts_to_convert = qw(
			     start_position
			     end_position
			     transcript_start
			     transcript_end
			     feat_chr_start
			     feat_chr_end
			     gene_chrom_start
			     gene_chrom_end
			     transcript_chrom_start
			     transcript_chrom_end
			     exon_chrom_start
			     exon_coding_end
			     exon_chrom_end
			     exon_coding_start
			     chromosome_location
			     );
    my $attribute_order = $self->get('original_attributes');
    my $attribute_number = 0;
    my ($orig_attribute,$position,$new_position);
    foreach (@$attribute_order){
	$orig_attribute = $_->name;
	foreach (@atts_to_convert){
	    if ($orig_attribute eq $_){
		# covert coordinates
		$position = $$row[$attribute_number];
		next if (!$position);
		my $db = $self->get('db_adaptor');
		my $sa = $db->get_SliceAdaptor();

               # create an analysis for the type of feature you wish to store
		my $analysis = new Bio::EnsEMBL::Analysis(
							  -LOGIC_NAME => 'your_analysis'
							  );
		my $slice_oldasm = $sa->fetch_by_region('chromosome', $chromosome, undef, undef,
							undef, $current_assembly);



		# create a new feature on the old assembly
		my $feat = Bio::EnsEMBL::SimpleFeature->new(
							    -DISPLAY_LABEL  => '',
							    -START          => $position,
							    -END            => $position,
							    -STRAND         => $strand,
							    -SLICE          => $slice_oldasm,
							    -ANALYSIS       => $analysis,
					      );

		# project feature to new assembly
		my $feat_slice = $feat->feature_Slice;
                my @segments;
                if ($feat_slice){
                    @segments = @{ $feat->feature_Slice->project('chromosome', $new_assembly) };
                }


		# do some sanity checks on the projection results:
		# discard the projected feature if
		#   1. it doesn't project at all (no segments returned)
		#   2. the projection is fragmented (more than one segment)
		#   3. the projection doesn't have the same length as the original
		#      feature

		if (scalar(@segments) != 1){
		    $new_position = '-';
		}
		elsif ($segments[0]->to_Slice()->length != $feat->length){
		    $new_position = '-';
		}
		elsif ($segments[0]->to_Slice()->seq_region_name ne $feat->slice->seq_region_name){
		    $new_position = '-';
		}
		else{
		    $new_position = $segments[0]->to_Slice()->start;
		}

		$$row[$attribute_number] = $new_position;
	    }
	}
	$attribute_number++;
    }

    # Escape delimiters in value-strings
    foreach(@{$row}) {
	$_ = q{} unless defined ($_);
	$_ =~ s/$FIELD_DELIMITER/\$FIELD_DELIMITER/g;
    }
    my $new_row_length = @$row - 3;
    $row = [@$row[0..$new_row_length]];

    # Create the final record-string
    return join($FIELD_DELIMITER, @{$row}) . $RECORD_DELIMITER;

}

sub processQuery {

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

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