> Hi, > I don't know if this is the appropriate forum to post this question, but since it's libwww-related (involves LWP) and I've tried other forums without success, I might as well give this one a go. > I'm trying to query Genemark > (http://genemark.biology.gatech.edu/GeneMark/webgenemark.html), a gene > prediction program, from the Unix shell with a Perl script. Yes, I know I > could paste in the sequences and 'run' the software from the web page > itself, but I've got hundreds of sequences to input, too many to do > manually. > > Anyway, I've created the following user, request, and response objects: > > use LWP::UserAgent; > use HTTP::Request::Common qw(POST); > $ua = new LWP::UserAgent; > > my $req = new POST => > 'http://exon.biology.gatech.edu/GeneMark/bin/webgenemark.cgi'; > Content_Type => 'text/html', > Content => [species => 'A.thaliana', > window => '96', > step => '12', > threshold => '0.5', > l_orfs => 'ORFs', > sequence => $a_sequence, > B1 => 'Start Genemark' > ]; > > while (1) { > $res = $ua->request($req); > > if ($res->is_success) { > last; > }; > }; > > @results = split /\n/, $res->content; > print $res->content; > > $a_sequence is a sequence of "A"s, "T"s, "G"s, and "C"s you can randomly > distribute as a test case. When I run the script, it doesn't return the > same results the web page does. In fact, it returns an html with no > results. Am I calling Genemark.hmm incorrectly, inputting the parameters > wrong, or what? Admittedly, I don't know how to handle 'text/html' forms, > so I'm sure I'm structuring the request wrong. > > Another website I'm having trouble with is Genscan > (http://genes.mit/edu/GENSCAN.html), another gene prediction program. I > get no response from their mail server, so please don't suggest I try > using that. The following code: > > use LWP::UserAgent; > $ua = new LWP::UserAgent; > $ua->agent("AgentName/0.1 " . $ua->agent); > > my $req = new HTTP::Request POST => > 'http://genes.mit.edu/cgi-bin/genescanw.cgi'; > $req->content_type('multipart/form-data'); > $req->content([-o => Arabidopsis, -n => $a_sequence, -p => 'Predicted > CDS and peptides', submit => 'Run GENSCAN']); > > my $res = $ua->request($req); > > while (1) { > $res = $ua->request($req); > > if ($res->is_success) { > last; > }; > }; > > @results = split /\n/, $res->content; > print $res->content; > > doesn't return anything--at least not the same thing as the webpage > itself. When I input a 'www-xxx-url-encoded' version into the > 'www-xxx-url-encoded' site, http://genes.mit.edu/oldGENSCAN.html, it just > returns the message: 'gform: Error This program can only be used to decode > forms'. I don't understand what's going on with either site. > > Any help would be greatly appreciated. Please e-mail responses to > [EMAIL PROTECTED] Thanks. > > > ---Brian Tam
