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

Sun May 29 22:41:50 EDT 2005

Thanks all.  I tried the both "SEQPASTE" and "seqpaste". but it did not work.   

Also, I modified the script according to Marc 's advice.

 my $response = $browser->post('http://www.cbs.dtu.dk/cgi-bin/nph-webface',
                       {"configfile" =>
"/usr/opt/www/pub/CBS/services/ChloroP-1.1/chlorop.cf",
                       	"SEQPASTE" => "$input_sequence",
                       	 "SEQSUB" => "",
                         "full" => "full",
                       	"submit" => "Submit"
                       	} );

unfortunately,  it still did work.

The problem is still complain that "Read: Field not declared; 'seqpaste'"

What's more interesiting, when I move the hidden value to another
place. It complains differently

my $response = $browser->post('http://www.cbs.dtu.dk/cgi-bin/nph-webface',
                       {
                       	"SEQPASTE" => "$input_sequence",
                       	 "SEQSUB" => "",
                         "full" => "full",
                          "configfile" =>
"/usr/opt/www/pub/CBS/services/ChloroP-1.1/chlorop.cf",
                       	"submit" => "Submit"
                       	} );

Complain:  Read: Field not declared; 'submit'

--------------I believe the problem is due to this sentence, but i do
not know what it is and where it is :-(

On 5/30/05, Marc Logghe <Marc.Logghe at devgen.com> wrote:
> 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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