RE: please help me to check why this perl script does not work!



> -----Original Message-----
> From: Bob Showalter [mailto:bob_showalter@xxxxxxxxxxxxxxx]
> Sent: Sunday, May 29, 2005 5:41 AM
> To: Fei Li; beginners@xxxxxxxx
> Subject: Re: please help me to check why this perl script
> does not work!
>
> Fei Li wrote:
> > 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>
>
> [snip]
>
> > my $response =
> > $browser->post('http://www.cbs.dtu.dk/cgi-bin/nph-webface',
> > [ "SEQPASTE" => "$item",
> > "submit" => "Submit"]
> > );
>
> Just, a guess, but you're passing "SEQPASTE" when perhaps you
> should be passing "seqpaste"?
>
>
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>
Assuming that was the case, here is what should be a much faster version of
the same code.

UNTESTED:

#!/usr/bin/perl

use warnings;
use strict;

use HTTP::Request::Common;
use LWP::UserAgent;

my $browser = LWP::UserAgent->new;

my $infile = "my_test_file"; #input my Fasta file

open( INPUT, "$infile" ) or die "can not open $infile: $!";
my $total = <INPUT>;
open( OUTPUT, ">>$infile.ChloroP.res" ) or die "Cannot create the output
file: $!";

while (<INPUT>) {
chomp;
my $response =
$browser->post('http://www.cbs.dtu.dk/cgi-bin/nph-webface',
[ "seqpaste" => "$_", "submit" => "Submit"]
);

if ($response->is_success) {
print OUTPUT "$response->content\n";
print OUTPUT "\n*********************************\n\n\n";
} else {
warn "WARN!: ", $response->status_line, "\n";
}

print "$. of $total finished\n";
}

close OUTPUT;
close INPUT;

Chris
.