[Milan-pm] (no subject)

[Paola Bisignano]

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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