[Bioperl-l] SMART domain sequence images

[Stephen L. Mathias]

John,

I would try writing your output to a filehandle which is explicitly set
to binary mode:

open OUT < $file or die "Can't open file:$!\n";
binmode OUT;
...
print OUT resp->content();
...
close OUT;

HTH.

-Steve

On Tue, 2004-05-11 at 09:59, john herbert wrote:
> Hello BioPerlers.
> I am working on a smallish set of peptides and would like to bulk
> download all the SMART domain pngs from the SMART website. Is there
> anything in BioPerl for this? Or does anyone know how I could capture
> the PNG files generated on sequences containing SMART domains from
> SMART's website. 
> 
> Here is an LWP script I tried using:
> #!/usr/local/bin/perl
> 
> use strict;
> use lib
> '/usr/ngasi/contexts/jakeysnakey/jakeysnakey/NewPerlLib/lib/perl5/site_perl';
> use LWP::UserAgent;
> use HTTP::Headers;
> use URI::URL;
> use HTTP::Request;
> 
> my $hders = HTTP::Headers->new(Accept => 'image/png');
> my $url =
> qq(http://smart.embl-heidelberg.de/smart/DD2.cgi?smart=428:DEXDc(64|265)+HELICc(301|382)+"%20border=0%20usemap="#map00"%20ALT="Bubblogram");
> 
> 
> my $url_ob = URI::URL->new($url);
> my $req = HTTP::Request->new('POST',$url_ob,$hders);
> my $ua = LWP::UserAgent->new();
> my $resp = $ua->request($req);
> if($resp->is_success){
>   print $resp->content();
> }else{
>   print $resp->message();
> }
> 
> 
> I have tried using this LWP script which works in the fact that it does
> collect the png binary data but it will not open as a png file. If I
> compare the file I have collected with my script, than with one I have
> attained by right clicking in windows explorer and saved to my desktop,
> there are some differences. I have no idea why they would be different.
> 
> 
> If there are anyone who has any ideas on this, I would be grateful.
> thanks.
> 
> John.
> 
> 
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-- 
(  Stephen L. Mathias, Ph.D.                   (                    (
 ) Office of Biocomputing                       )                    )
(  University of New Mexico School of Medicine (   s m a t h i a s  (
 ) MSC08 4560                                   )  @ u n m . e d u   )
(  1 University of New Mexico                  (                    (
 ) Albuquerque, NM 87131-0001                   )                    )