[Milan-pm] (no subject)

[Paola Bisignano]

thank you....I'm start programming with Perl and it's only a month...I'm
very new.... and i couldn't get

2009/4/1 marcos rebelo <oleber at gmail.com>

> 2009/4/1 Paola Bisignano <paola.bisignano at gmail.com>:
> >
> > #!/usr/local/bin/perl
> > use LWP::Simple;
> > use strict;
> > use warnings;
> > use LWP 5.64;
> > use LWP::UserAgent;
> > print "Quale entry di PDB vuoi aprire? ";
> > my $pdb=<STDIN>;
> > chomp ($pdb);
> > my $url1 =
> > "
> http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=$pdb
> ";
> > my $content = get $url1;
> > die "Couldn't get $url1" unless defined $content;
> > while ($content=~ m/uniprot_id=(.*?)&/g)
> >
> >     {
> >     my $code=$1;
> >     print "ID uniprot: $code\n";
> >     chomp ($code);
> >     my $browser =LWP::UserAgent->new;
> >     my $url = URI-> new ("http://www.uniprot.org/uniprot/$code.fasta");
> >     my $response=$browser-> get ($url);
> >     my $fasta=$response->content;
> >     print "$fasta" ;
> >     };
> >
> >
> >
> >
> >
> > this is my script...first I must digit the pdb code (form my test I use
> > 1xmj, that I'm sure it has a ligand) I want to explore, (that's the code
> of
> > a protein structure) and then I go to the web page...to extract another
> > code, that'uniprot code, so the script thakes that code and put it into
> > another web site and estract and print the  aminoacidic sequence of the
> > protein, then i need to know something about the ligand...and  I need to
> > access to the file  running.pl that brings some information which I have
> to
> > extract....and i don't know what to do
> >
> > _______________________________________________
> > Milan-pm mailing list
> > Milan-pm at pm.org
> > http://mail.pm.org/mailman/listinfo/milan-pm
> >
> >
>
> your code is similar to this simpler code:
>
> #!/usr/local/bin/perl
> use strict;
> use warnings;
> use LWP::Simple;
>
> print "Quale entry di PDB vuoi aprire? ";
> my $pdb = <STDIN>;
> chomp ($pdb);
> my $url = "
> http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=$pdb
> ";
> my $content = get($url);
> die "Couldn't get $url" unless defined $content;
> foreach my $code ( $content =~ m/uniprot_id=(.*?)&/g) {
>     print "ID uniprot: $code\n";
>    chomp ($code);
>     my $fasta=get("http://www.uniprot.org/uniprot/$code.fasta");
>    print "$fasta" ;
> };
>
>
> Now, you need to explain your problem to someone that doesn't know
> anything about this bio stuff.
>
> Best Regards
> Marcos Rebelo
>
> --
> Marcos Rebelo
> http://oleber.freehostia.com
> Milan Perl Mongers leader http://milan.pm.org
> _______________________________________________
> Milan-pm mailing list
> Milan-pm at pm.org
> http://mail.pm.org/mailman/listinfo/milan-pm
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.pm.org/pipermail/milan-pm/attachments/20090402/c0e60dca/attachment.html>