[Milan-pm] (no subject)

[Paola Bisignano]

I've sent the file I need to automatically download....because I think It's
the easiest way to explain my trouble.....and I'm actually asking for
help...and I want to apologize to insist on

2009/4/2 Paola Bisignano <paola.bisignano at gmail.com>

> I want to thank to everyone for help...I hope I will learn soon how to
> program...and help people who need to!!!!!!!!!!!!!
>
>
> 2009/4/2 Paola Bisignano <paola.bisignano at gmail.com>
>
>> now I will send the file I need to automatically download....I downloaded
>> it manually, that's the runligplot.pl....because I need to automatically
>> access to the script....to extract information about amminoacidic
>> connections between ligand and receptor...
>>
>> 2009/4/2 Paola Bisignano <paola.bisignano at gmail.com>
>>
>> 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
>>>>
>>>
>>>
>>
>
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