Question

I have an ID code representative of a protein. There is website called InterPro that is used to deal with proteins related information. URL for that website contains that particular code. By changing that code in that URL I can get information about any protein. I developed a script in perl to get information directly from web. I used following code

    my $uniprot= "P15700";
    my $resp= '';
    my $url= "http://wwwdev.ebi.ac.uk/interpro/ISearch?query=$uniprot+";
    my $file = "$uniprot";
    $resp = getstore( $url, $file ); 


exit;
}

In this example P15700 is that unique ID of protein and the url is http://wwwdev.ebi.ac.uk/interpro/ISearch?query=P15700+. Now this will retrieve whole html page. But, I need a particular information on that page which under the heading of “protein family membership”. Like in this example If you open this link you can find “Adenylate kinase” written under heading of protein family membership. I just neeed to that information in another output text file displaying a table in which one column says ID and other says that information under protein family membership.
I am new to perl and I don’t have computer science background. Rather I am a biologist. So, I want to know whether the above mentioned task can be done using perl. If yes, How?
I ll be grateful if anyone can solve this problem.

Answer 1

Not even sexy, but it works (based on HTML::Treebuilder Module) – you have to parse the HTML and extract the information. In this example the result will be stored as csv in the File “result.txt”

use LWP::Simple;
use HTML::TreeBuilder;

my $uniprot= "P15700";
my $url= "http://wwwdev.ebi.ac.uk/interpro/ISearch?query=$uniprot+";
my $resp = get( $url );

my $tree = HTML::TreeBuilder->new_from_content($resp);
my $first=$tree->look_down(_tag => 'div',class => 'prot_fam') ;
$first=$first->look_down(_tag => 'div',class => 'entry-parent');
$first=$first->look_down(_tag => 'div',class => 'entry-parent');
$first=$first->look_down(_tag => 'a');
open (FH,">>result.txt");
print FH $uniprot.";";
print FH $first->content_list;
print FH "\n";
close(FH);

Edit:
Here’s a variant for checking lot’s of “uniprots”. Play around with the sleepdelay

use LWP::Simple;
use HTML::TreeBuilder;

my @ports=qw(Q9H4B7 Q96RI1 P04150 P35354 P23219 P61073 P0A3M6 Q8DR59 Q7CRA4 Q27738 P35367 P35367 P35367 P08172 P35367 P10275 P25021 P07550 P08588 P13945);

for (my $i=0;$i < scalar(@ports);$i++) {
my $url= "http://wwwdev.ebi.ac.uk/interpro/ISearch?query=".$ports[$i]."+";
my $resp = get( $url );

my $tree = HTML::TreeBuilder->new_from_content($resp);
my $first=$tree->look_down(_tag => 'div',class => 'prot_fam') ;
$first=$first->look_down(_tag => 'div',class => 'entry-parent');
$first=$first->look_down(_tag => 'div',class => 'entry-parent');
$first=$first->look_down(_tag => 'a');
open (FH,">>result.txt");
print FH $ports[$i].";";
print FH $first->content_list;
print FH "\n";
close(FH);
sleep 10;
}