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lib/Bio/Homology/InterologWalk.pm  view on Meta::CPAN

                       exp_only   => $exp_only,
                       phys_only  => $physical_only
                       );

     my $missed = 0;
     while (<$in_data>){
          my ($ID) = $_;
          chomp $ID;
          next if ($ID eq '');
          
#          my $idsignature;
          #get a "signature" to spot the kind of id we are dealing with.
          #current solution involves getting all the letters starting from the beginning, if there's at least two.
          #otherwise get the initial three characters whatever they are, and then do a fuzzy regex matching using string::approx
          #this will be needed in order to be sure to get the same kind of id back.
          #eg "IPR006259" ----> "IPR"
#          if($ID =~ /^([a-z]{2,})(.+)/i){
#               $idsignature = $1;
#          }else{
#               $idsignature = substr($ID, 0, 1) . substr($ID, 1, 1) . substr($ID, 1, 1);
#          }
          
          print "$ID: Querying IntAct WS for $ID..";
          my $request = $url . $int_search_string.  $ID . $options;
          
          $client->GET($request);
          print "(", $client->responseCode(), ")";
          
          my $responseContent = $client->responseContent();
          if(!$responseContent){

lib/Bio/Homology/InterologWalk.pm  view on Meta::CPAN

                                                    alt_id_b         => $DF_alt_id_b,
                                                    name_a           => $DF_name_a,  
                                                    name_b           => $DF_name_b,
                                                    props_a          => $DF_props_a,
                                                    props_b          => $DF_props_b,
                                                    adaptor          => $gene_adaptor,
                                                    id_check         => $ID_check                                                   
                                                    );
               #fuzzy string matching: this ID_OUT should be of the same kind as the original id. Does it feature the same initial
               #id signature or something very close?
               #if(!_fuzzy_match($idsignature, $ID_OUT)){
               #     $ID_OUT = _get_ensembl_id_from_uniprotkb_id($gene_adaptor, $target_AccNumb, $target_Name, $target_Aliases, $target_PropsRow);
               #}
               #TODO REVIEW THIS                                    

               if($ID_OUT){
                    print("Interaction ($DF_interaction_id): $ID <--> $ID_OUT\n");
                    my $fullDataRow = join("\t",$ID,$DF_interaction_id,
                                        $DF_acc_numb_a, $DF_acc_numb_b,
                                        $DF_alt_id_a, $DF_alt_id_b,
                                        $DF_name_a, $DF_name_b,