New parsing of the description, remving RecName: etc..

misc-scripts/xref_mapping/XrefParser/UniProtParser.pm

@@ -301,17 +301,109 @@ sub create_xrefs {
     @all_lines = split /\n/, $description_and_rest;
 
     # extract ^DE lines only & build cumulative description string
-    my $description;
+    my $description = " ";
+    my $name        = "";
+    my $flags       = " ";
+
+    my $mode = "";
+
     foreach my $line (@all_lines) {
-      my ($description_only) = $line =~ /^DE\s+(.+)/;
-      $description .= $description_only if ($description_only);
-      $description .= " ";
+
+      next if(!($line =~ /^DE/));
+
+
+      # Set up the mode first
+      if($line =~ /^DE   RecName:/){
+	if($mode eq "RecName"){
+	  $description .= ";";
+	}	
+        $mode = "RecName";
+      }
+      elsif($line =~ /^DE   SubName:/){
+	if($mode eq "RecName"){
+	  $description .= ";";
+	}	
+        $mode = "RecName";
+      }
+      elsif($line =~ /^DE   AltName:/){
+        $mode = "AltName";
+      }
+      elsif($line =~ /^DE   Contains:/){
+	if($mode eq "Contains"){
+	  $description .= ";";
+	}
+        elsif($mode eq "Includes"){
+          $description .= "][Contains ";
+        }
+	else{
+          $description .= " [Contains ";
+        }	
+        $mode = "Contains";
+        next;
+      }
+      elsif($line =~ /^DE   Includes:/){
+	if($mode eq "Includes"){
+	  $description .= ";";
+	}	
+        elsif($mode eq "Contains"){
+          $description .= "][Includess";
+        }
+	else{
+          $description .= " [Includes ";
+        }	
+        $mode = "Includes";
+        next;
+      }
+      elsif($line =~ /^DE   Flags: (.*);/){
+        $flags .= "$1 ";
+        next;
+      }
+
+
+      # now get the data
+      if($line =~ /^DE   RecName: Full=(.*);/){
+        $name .= $1;
+      }
+      elsif($line =~ /RecName: Full=(.*);/){
+        $description .= $1;
+      }
+      elsif($line =~ /SubName: Full=(.*);/){
+        $name .= $1;
+      }
+      elsif($line =~ /AltName: Full=(.*);/){
+        $description .= "(".$1.")";        
+      }
+      elsif($line =~ /Short=(.*);/){
+        $description .= "(".$1.")";        
+      }
+      elsif($line =~ /EC=(.*);/){
+        $description .= "(EC ".$1.")";        
+      }
+      elsif($line =~ /Allergen=(.*);/){
+        $description .= "(Allergen ".$1.")";        
+      }
+      elsif($line =~ /INN=(.*);/){
+        $description .= "(".$1.")";        
+      }
+      elsif($line =~ /Biotech=(.*);/){
+        $description .= "(".$1.")";        
+      }
+      elsif($line =~ /CD_antigen=(.*);/){
+        $description .= "(".$1." antigen)";        
+      }
+      else{
+         print STDERR "unable to process *$line* for $acc\n";
+      }
+
+    }
+    if($mode eq "Contains" or $mode eq "Includes"){
+      $description .= "]";
     }
 
     $description =~ s/^\s*//g;
     $description =~ s/\s*$//g;
 
-    $xref->{DESCRIPTION} = $description;
+    $xref->{DESCRIPTION} = $name.$flags.$description;
 
     # extract sequence
     my ($seq) = $_ =~ /SQ\s+(.+)/s; # /s allows . to match newline

misc-scripts/xref_mapping/XrefParser/UniProtParser_descriptions_only.pm

@@ -280,18 +280,105 @@ sub create_xrefs {
     @all_lines = split /\n/, $description_and_rest;
 
     # extract ^DE lines only & build cumulative description string
-    my $description;
+    my $description = " ";
+    my $name        = "";
+    my $flags       = " ";
+
+    my $mode = "";
     foreach my $line (@all_lines) {
-      my ($description_only) = $line =~ /^DE\s+(.+)/;
-      $description .= $description_only if ($description_only);
-      $description .= " ";
+
+      next if(!($line =~ /^DE/));
+
+      # Set up the mode first
+      if($line =~ /^DE   RecName:/){
+	if($mode eq "RecName"){
+	  $description .= "; ";
+	}	
+        $mode = "RecName";
+      }
+      elsif($line =~ /^DE   SubName:/){
+	if($mode eq "RecName"){
+	  $description .= "; ";
+	}	
+        $mode = "RecName";
+      }
+      elsif($line =~ /^DE   AltName:/){
+        $mode = "AltName";
+      }
+      elsif($line =~ /^DE   Contains:/){
+	if($mode eq "Contains"){
+	  $description .= "; ";
+	}
+        elsif($mode eq "Includes"){
+          $description .= "][Contains ";
+        }
+	else{
+          $description .= " [Contains ";
+        }	
+        $mode = "Contains";
+        next;
+      }
+      elsif($line =~ /^DE   Includes:/){
+	if($mode eq "Includes"){
+	  $description .= "; ";
+	}	
+        elsif($mode eq "Contains"){
+          $description .= "][Includess";
+        }
+	else{
+          $description .= " [Includes ";
+        }	
+        $mode = "Includes";
+        next;
+      }
+      elsif($line =~ /^DE   Flags: (.*);/){
+        $flags .= "$1 ";
+        next;
+      }
+
+      # now get the data
+      if($line =~ /^DE   RecName: Full=(.*);/){
+        $name .= $1;
+      }
+      elsif($line =~ /RecName: Full=(.*);/){
+        $description .= $1;
+      }
+      elsif($line =~ /SubName: Full=(.*);/){
+        $name .= $1;
+      }
+      elsif($line =~ /AltName: Full=(.*);/){
+        $description .= "(".$1.")";        
+      }
+      elsif($line =~ /Short=(.*);/){
+        $description .= "(".$1.")";        
+      }
+      elsif($line =~ /EC=(.*);/){
+        $description .= "(EC ".$1.")";        
+      }
+      elsif($line =~ /Allergen=(.*);/){
+        $description .= "(Allergen ".$1.")";        
+      }
+      elsif($line =~ /INN=(.*);/){
+        $description .= "(".$1.")";        
+      }
+      elsif($line =~ /Biotech=(.*);/){
+        $description .= "(".$1.")";        
+      }
+      elsif($line =~ /CD_antigen=(.*);/){
+        $description .= "(".$1." antigen)";        
+      }
+      else{
+         print STDERR "unable to process *$line* for $acc\n";
+      }
+    }
+    if($mode eq "Contains" or $mode eq "Includes"){
+      $description .= "]";
     }
 
     $description =~ s/^\s*//g;
     $description =~ s/\s*$//g;
 
-    $xref->{DESCRIPTION} = $description;
-
+    $xref->{DESCRIPTION} = $name.$flags.$description;
 
 
     push @xrefs, $xref;