[Bioperl-l] how to create Graphics object from home-made SQL table with parsed blast data?

[Jan Aerts]

Hi Marcus,

I would start creating a GFF file based on your database, and visualize
that using either gbrowse (http://www.gmod.org/ggb/gbrowse.shtml) or a
custom script. A step-by-step procedure to write such a script using the
bioperl package is available at
http://bioperl.org/HOWTOs/Graphics-HOWTO/index.html.

jan. 

On Fri, 2004-10-29 at 05:17, Marcus Claesson wrote:
> Hi there,
> 
> My apologies if this already has been adressed in this list. I have a
> number of mysql tables with blast data that I parsed using Bio::SearchIO
> (see below). I now want to use that data to create graphics overviews in
> png-format with the Bio::Graphics module. I guess the normal way for
> doing this is by implementing Bio::SeqFeature to the
> Bio::Graphics::Panel class. However, all blast-outputs are already
> parsed and put into a table and I would like to use that format. Is
> there any way of using these tables instead of the Bio::SeqFeature
> module?
> 
> Here is how it was parsed and put into the table:
> 
>     $in = new Bio::SearchIO(-format => 'blast', 
>                             -file     => 'blast_output.txt');
> 
>     $dbh->do("CREATE TABLE $table(format TEXT NOT NULL,sbj_name TEXT NOT
> NULL,sbj_count INTEGER,hsp_count INTEGER,hsp_length INTEGER,E_value
> DOUBLE PRECISION,score INTEGER,bits REAL,percent_id REAL,query_begin
> INTEGER,query_end INTEGER,sbj_length INTEGER,sbj_begin INTEGER,sbj_end
> INTEGER,frame CHAR(3),alignment TEXT)") unless ($add eq "yes");
>     $sth = $dbh->prepare("INSERT INTO $table VALUES
> (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)");
>     while($result = $in->next_result) {
> 	$sbj_count = 0;
> 	while($hit = $result->next_hit) {
> 	    $sbj_count++;
> 	    my $hsp_count = 0;
> 	    my $sbj_name = $hit->name." ".$hit->description;
> 	    $sbj_name =~ s/'/\\'/gi;
> 	    my $sbj_length = $hit->length('query');
> 	    while($hsp = $hit->next_hsp ) {
> 		$hsp_count++;
> 		if ($format eq "blast") {
> 		    $frame_value = ($hsp->query->frame + 1) * $hsp->query->strand;
> 		} elsif ($format eq "fasta") {
> 		    $frame_value = "+" if ($hsp->query->strand eq "1");
> 		    $frame_value = "-" if ($hsp->query->strand eq "-1");
> 		}
> 		my $align = "Query -->\n".
> 		    $hsp->query_string."\n".
> 		    $hsp->homology_string."\n".
> 		    $hsp->hit_string."\n".
> 		    "Subject -->\n";
> 		my $evalue = $hsp->evalue;
> 		$evalue =~ s/^e/1e/gi;
> 		my $score = $hsp->score;
> 		my $bits = $hsp->bits;
> 		my $percent_id = $hsp->percent_identity;
> 		my $hsp_length = $hsp->length('total');
> 		my $query_begin = $hsp->query->start + $offset;
> 		my $query_end = $hsp->query->end + $offset;
> 		my $sbj_begin = $hsp->hit->start;
> 		my $sbj_end = $hsp->hit->end;
> 
> 		$sth->execute($format,$sbj_name,$sbj_count,$hsp_count,$hsp_length,$evalue,$score,$bits,$percent_id,$query_begin,$query_end,$sbj_length,$sbj_begin,$sbj_end,$frame_value,$align);
> 	    }
> 	}
> 
> 
> Many thanks in advance!
> 
> Marcus
> 
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