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Summary

BioMart::Formatter::FASTACDNA

Package variables

Inherit

BioMart::FormatterI

Synopsis

The FASTA Formatter returns whitespace separated tabular data
for a BioMart query's ResultTable

Description

When given a BioMart::ResultTable containing the results of
a BioMart::Query the FASTA Formatter will return tabular output
with one line for each row of data in the ResultTable and single spaces
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();

}

sub getDisplayNames {

    my $self = shift;

    return '';

}

sub isSpecial {

    return 1;
}

1;

}

sub nextRow {

    my $self = shift;

    my $rtable = $self->get('result_table');
    my $row = $rtable->nextRow;
    if (!$row){
        return;
    }
    
     
    #my $array_length = @{$row};
    my ($OUTPUT, $SEQOUT, $tot,$firstexonstart);

    my $seq = ${$row}[0];
    my $structure = ${$row}[1];
    my $strand = ${$row}[2];
    my @exons = split(/\|/, $structure);
       
    #- reverse the array in the right order if strand -1
    if ($strand < 0){ @exons = reverse @exons}
    
    
    foreach my $exon (@exons){
	#print "$exon\n";
	my ($start, $end, $strand, $phase) = split (/:/,$exon);
	if (!$firstexonstart) {$firstexonstart = $start;}
	print "firstexonstart: $firstexonstart\n";
	
	#$firstexonstart = "178090562";
	my $tmp_start = $start - $firstexonstart ;print "tmp_start: $tmp_start\n";
	my $tmp_end = $end - $firstexonstart +1 ;print "tmp_end: $tmp_end\n";
	my $length =  $end - $start +1 ;

	$SEQOUT .=  substr($seq,$tmp_start,$length);
	#print "length: $length\n";
	#$tot += $length ;


    }
    #print "tot: $tot\n";

    
    my @tab = split (//,$SEQOUT);
    my $size = @tab ;
    if ($strand < 0){$SEQOUT = &rc($SEQOUT)}
    return $SEQOUT."\n";
    
    #map { $_ ||= ''; } @$row; # get rid of unitialized-value warning message
    #my $header_atts = join "|",@{$row}[1..$array_length-1];
    #chop $header_atts;
    #my $seq = ${$row}[0];
    #$seq =~ s/(\w{60})/$1\n/g;
    #return ">" . $header_atts . "\n"
#	       . $seq ."\n";

}

sub processQuery {

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

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

}

sub rc {

    my ($seq) = shift;
    #warn "Enter _rc\n";
    $seq = reverse($seq);
    $seq =~ tr/YABCDGHKMRSTUVyabcdghkmrstuv/RTVGHCDMKYSAABrtvghcdmkysaab/;
    return $seq;

}

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