[Bioperl-l] Question on integrating Bio::Graphics with Bio::SearchIO::Writer::HTMLResultWriter

Anand Venkatraman bioperlanand at yahoo.com
Wed Apr 23 02:02:30 EDT 2008


Hi everybody,

I would like to use Bio::Graphics in conjunction with Bio::SearchIO::Writer::HTMLResultWriter to obtain a HTML formatted blast report output along with an image 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 am able to get the HTML output using  "Bio::SearchIO::Writer::HTMLResultWriter" and I am able to get the image using the examples outlined in the Bio::Graphics HOWTO: http://www.bioperl.org/wiki/HOWTO:Graphics

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

I also found that someone else has asked something similar to whatever I am asking & is listed under the "Orphans, Leftovers" category in the ListSummary:April 26-May 9,2006 document: 
http://www.bioperl.org/wiki/ListSummary:April_26-May_9%2C2006#Orphans.2C_Leftovers

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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