[Milan-pm] (no subject)

[Paola Bisignano]

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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