[Bioperl-l] please help me to check why this perl script does
notwork!
Marc Logghe
Marc.Logghe at devgen.com
Mon May 30 03:08:53 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.
That is odd. In my hands it works. I'll attach the complete script.
The output is:
<HTML>
<HEAD><TITLE>Webface Jobsubmission</TITLE></HEAD>
If Javascript is disabled, follow <a
href="http://www.cbs.dtu.dk/cgi-bin/nph-webface?jobid=chlorop,429AB96A0C
8A9C29&opt=wait">This link</a>
<script LANGUAGE="JavaScript"><!--
location.replace("http://www.cbs.dtu.dk/cgi-bin/nph-webface?jobid=chloro
p,429AB96A0C8A9C29&opt=wait")
//--></script>
</HTML>
*********************************
HTH,
Marc
>
> 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;
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> >
>
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