[Bioperl-l] a question on obtaining HTML formatted Blast output along with the Blast hits image

Anand Venkatraman bioperlanand at yahoo.com
Mon Apr 21 03:44:00 EDT 2008


 Hi everybody,

I would like to obtain a HTML formatted blast report output along with a picture of the blast hits as shown on Slide 60 in this pdf: http://jason.open-bio.org/Bioperl_Tutorials/NESCENT_2007/CSHL_Bioperl_I.pdf

I have gotten the HTML output working using "Bio::SearchIO::Writer::HTMLResultWriter".

My question: How do I integrate it with Bio:Graphics to render the blast hits image at the correct position in my Bioperl reformatted html file.

I ultimately want to be able to display my blast output files on a browser. 

Here is my code so far:
----------------------------------------------------------------
#!/usr/bin/perl -w
# usage: $0 <blast_report>
use strict;
use Bio::SearchIO;
use Bio::SearchIO::Writer::HTMLResultWriter;

my $infile = shift or die $!;

my $searchio = new Bio::SearchIO( -format => 'blast',-file   => $infile );
my $writerhtml = new Bio::SearchIO::Writer::HTMLResultWriter();
my $outhtml = new Bio::SearchIO(-writer => $writerhtml,
                                -file   => ">${infile}.html");

$outhtml->write_result($searchio->next_result);
----------------------------------------------------------------

Thanks in advance,

Anand


       
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