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

Jason Stajich jason at bioperl.org
Thu Apr 24 14:06:41 EDT 2008


The overview graphic is generated basically from the script in  
scripts/graphics/search_overview.PLS

So you'd have to run that on each report to generate the graphic,  
then use the other methods  to insert <img src="NAME"> images into  
each rendered HTML report.

-jason

On Apr 23, 2008, at 4:05 PM, Anand Venkatraman wrote:

> Hi Jason,
>
> Thanks for the reply.
>
> I am a little lost with the solution suggested. Is that how slide  
> 60 in the pdf is obtained: http://jason.open-bio.org/ 
> Bioperl_Tutorials/NESCENT_2007/CSHL_Bioperl_I.pdf
>
> I guess I am missing something quite obvious, I apologize.
>
> What I have & want is this: I have a directory having say 100  
> different blast reports & hence I am looking to obtain 100  
> different bioperl formatted blast html outputs with the respective  
> images just as it would appear in the blast report.
>
> Thanks,
>
> Anand
>
> Jason Stajich <jason at bioperl.org> wrote:
>
> 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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