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

Jason Stajich jason at bioperl.org
Wed Apr 23 02:15:28 EDT 2008


Basically you want to inject your own IMG tags into the file with  
these routines:

     $writerhtml->start_report(\&my_start_report);
     $writerhtml->title(\&my_title);
     $writerhtml->hit_link_align(\&my_hit_link_align);
     $writerhtml->hit_link_desc(\&my_hit_link_desc);

fgblast shows a way to do this in part. It relies on Gbrowse to  
generate the image but you can replace the gbrowse_img reference to  
your own image generating software.

http://people.genome.duke.edu/~jes12/software/scripts/fgblast

-jason
On Apr 22, 2008, at 11:02 PM, Anand Venkatraman wrote:

> 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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