[Bioperl-l] please help me to check why this perl script does notwork!

Sun May 29 16:50:03 EDT 2005

Hi,
There are a few issues with the script:
1) @seq is not an array of (fasta) sequences, but in your case a list of
lines. This can be fixed like so:
#@seq = <INPUT>;
local $/ = undef;
@seq = split /\n(?=>)/, <INPUT>;

2) You have to POST all necessary parameters, including the hidden ones.
Also, apparently, you have to pass a hash ref in stead of an array ref
to post():
         my $response =
$browser->post('http://www.cbs.dtu.dk/cgi-bin/nph-webface',
                       { "SEQPASTE" => "$item",
                         full => 'full',
                         "configfile" =>
"/usr/opt/www/pub/CBS/services/ChloroP-1.1/chlorop.cf"
                       }
                         );

3) The resulting content is an html page with javascript in it and a url
where to fetch the result when finished. So I guess you have to parse
out that url and perform another request.

HTH,
Marc

Marc Logghe, PhD
deVGen NV
Technologiepark 30
B - 9052 Ghent-Zwijnaarde
Tel. +32 9 324 24 83 
Fax. +32 9 324 24 25 
Web: www.devgen.com

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> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org 
> [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Fei Li
> Sent: Sunday, May 29, 2005 9:37 AM
> To: Bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] please help me to check why this perl 
> script does notwork!
> 
> I wish to submit some protein sequences via LWP:UserAgent  to 
> the http://www.cbs.dtu.dk/services/ChloroP/
> 
> The error message is given as follows:
> 
> <HTML><HEAD><TITLE>Webface Error</TITLE></HEAD><font 
> color=red><h1>Webface Error: </h1><h4>
> Read: Field not declared; 'seqpaste'</h4> <br> </font></HTML>
> 
> *********************************
> 
> 
> #! /usr/bin/perl -w
> use strict;
> use HTTP::Request::Common;
> use LWP::UserAgent;
> 
> my $browser = LWP::UserAgent->new;
> my @seq;
> my $count =0;
> 
> my $infile = "my_test_file"; #input my Fasta file
> 
> open INPUT, "$infile" or die "can not open $infile:$!"; open 
> OUTPUT, ">>$infile.ChloroP.res" or die "Cannot create the 
> output file: $!";
> 
> @seq = <INPUT>;
> my $total = @seq;
> 
> foreach my $item (@seq){
>         $count ++;
>         chomp $item;
>          my $response =
> $browser->post('http://www.cbs.dtu.dk/cgi-bin/nph-webface',
>                        [ "SEQPASTE" => "$item",
>                        	 "submit" => "Submit"]
>                          );
>           warn "WARN!: ", $response->status_line, "\n" unless 
> $response->is_success;
> 
>           if($response->is_success){
>                   my $result = $response->content;
>                   open OUTPUT, ">>$infile.ChloroP.res" or die 
> "Cannot create the output file: $!";
>                   print OUTPUT "$result\n";
>                   print OUTPUT 
> "\n*********************************\n\n\n";
>             }
>   print "$count of $total finished\n";
>   }
> 
>  close OUTPUT;
>  close INPUT;
> 
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