Completed gene symbol feature; working on heat map feature

svn path=/; revision=185

diff --git a/preecej/perl_singletons/pathway_gene_swapper.pl b/preecej/perl_singletons/pathway_gene_swapper.pl
index 82d9812146e0c39b136da4455de32ee5f729e050..7f74b3a4e74a3b31735d5aab0b90dae3ea80c1b9 100644 (file)
--- a/preecej/perl_singletons/pathway_gene_swapper.pl
+++ b/preecej/perl_singletons/pathway_gene_swapper.pl
@@ -25,6 +25,10 @@ a new group will be created.
 If an original gene had multiple instances displayed on the pathway
 diagram, each instance will be subjected to the replacement process.
 
+There is also an option to read in an extra column of gene symbols, if the 
+user wishes to provide their own. Otherwise, the application will 
+continue to use the label prefix and auto-numbering suffix settings.
+
 The replacement gene symbols can be prefixed to separate them from the 
 original, and an ordinal suffix ('-#') will be added to a group of 
 replacement genes.
@@ -35,14 +39,12 @@ of cards).
 
 =head1 FUTURE CHANGES
 
-Add the option to read in an extra column of gene symbols, if the 
-user wishes to provide their own. Otherwise, continue to use the label
-prefix and auto-numbering suffix settings.
-
 Add a comment containing the NCBI species id of the new homolog (for 
 the purpose of multi-species pathway comparison or host-pathogen 
 interaction diagrams).
 
+Add a "heat-map" effect by making large paralog sets "hotter". 
+
 =head1 USAGE
 
 pathway_gene_swapper.pl -i INPUT_FILE -g GENE_FILE -c CONFIG_FILE -o OUTPUT_FILE -L -v -G -d
@@ -56,6 +58,8 @@ pathway_gene_swapper.pl -i INPUT_FILE -g GENE_FILE -c CONFIG_FILE -o OUTPUT_FILE
         (NOTE: if no path supplied for input files, 
         current working directory is assumed)
     -s  use provided gene symbols instead of config file's LabelPrefix
+    -h  apply a heat-map to any multi-mapped set of paralogs
+        (NOTE: precludes custom box-coloring via the config file)
     -L  Remove literature references.
     -v  View verbose information
     -G  Display GPML input/output documents
@@ -72,6 +76,10 @@ pathway_gene_swapper.pl -i INPUT_FILE -g GENE_FILE -c CONFIG_FILE -o OUTPUT_FILE
         
         The second column may have one and only one gene variant or 
         homolog -- the "replacement" gene(s).
+        
+        An optional "gene symbol" column may be placed between the 
+        first two columns, if the user would prefer to use a list of
+        symbols for the new homologous genes.
     
     - The config file may have any or all of the following entries,
       in addition to the required fields (in any order):
@@ -115,6 +123,7 @@ use Getopt::Std;
 use Data::Dumper;
 
 # specific
+use Graphics::ColorUtils qw( :gradients );
 use XML::DOM;
 
 # ---------------------------------------------------------------------------
@@ -127,6 +136,7 @@ my $input_gpml_file;
 my $input_gene_file;
 my $input_config_file;
 my $output_file;
+my $apply_paralog_heat = 0;
 my $remove_lit = 0; # flag to remove literature and lit references
 my $use_symbols = 0; # flag to indicate use of provided gene symbols
 my $verbose = 0; # flag for verbose output
@@ -219,7 +229,7 @@ screen output.
 sub init
 {
     # read and set options
-    getopts('i:g:c:o:LsvGd', \%opts);
+    getopts('i:g:c:o:hLsvGd', \%opts);
     
     foreach my $key (keys %opts) { 
         my $value = $opts{$key};
@@ -253,6 +263,7 @@ sub init
                 }
             }
             case "s" { $use_symbols = 1; }
+            case "h" { $apply_paralog_heat = 1; }
             case "L" { $remove_lit = 1; }
             case "v" { $verbose = 1; }
             case "G" { $doc_mode = 1; }
@@ -274,6 +285,7 @@ sub init
         . "Output File: $output_file\n"
         . "\n"
         . "Use provided gene symbols? " . ($use_symbols ? "Yes" : "No") . "\n"
+        . "Provide paralog heat-map? " . ($apply_paralog_heat ? "Yes" : "No") . "\n"
         . "Remove literature references? " . ($remove_lit ? "Yes" : "No") . "\n"
         . "Running in verbose mode? " . ($verbose ? "Yes" : "No") . "\n"
         . "Running in document mode? " . ($doc_mode ? "Yes" : "No") . "\n"
@@ -650,20 +662,17 @@ sub swap_genes
                     }
                     
                     my $curr_new_node = $$_[0];
-                    my $curr_symbol = "";
-
-                    if ($use_symbols)
-                    {
-                        $curr_symbol = ${$$_[1]}[0];
-                    }
-
-                    my $curr_homolog = ${$$_[1]}[1];
+                    my $curr_symbol = ${$$_[1]}{"symbol"};
+                    my $curr_homolog = ${$$_[1]}{"new_item"};
 
                     #print "$_: $curr_new_node, $curr_symbol, $curr_homolog\n"; # TEST
                     #print "[Curr New Node before editing...]\n" . $curr_new_node->toString . "\n\n"; # TEST
 
                     # update all new nodes w/ attributes...
-    
+
+                    # grab original text label
+                    my $old_label = $curr_new_node->getAttributeNode("TextLabel")->getValue;
+                    
                     # rename TextLabel...
                     if ($use_symbols && length($curr_symbol) > 0) # apply the provided gene symbol
                     {
@@ -687,7 +696,7 @@ sub swap_genes
                     # NOTE: order is important in GPML; the <Comment> tags are first
                     my $new_comment = $gpml_doc->createElement("Comment");
                     $new_comment->setAttribute("Source",$configs{"Source"});
-                    $new_comment->addText($configs{"CommentPrefix"} . " $old_gene.");
+                    $new_comment->addText($configs{"CommentPrefix"} . " $old_gene ($old_label).");
                     $curr_new_node->insertBefore($new_comment,$curr_new_node->getFirstChild); # assumes other child nodes  
                     
                     # edit <Xref Database="JGI" ID="Egrandis..." />
@@ -700,8 +709,17 @@ sub swap_genes
                     $curr_graphics->setAttribute("Width",$configs{"BoxWidth"});
                     if ($configs{"BoxBorder"}) {
                         $curr_graphics->setAttribute("Color",$configs{"BoxBorder"}); }
-                    if ($configs{"BoxColor"}) {
-                        $curr_graphics->setAttribute("FillColor",$configs{"BoxColor"}); }
+
+                    # add "heat" to genes with multiple paralogs
+                    if ($apply_paralog_heat && ($gene_suffix_counter > 0))
+                    {
+                        $curr_graphics->setAttribute("FillColor","cc0000");
+                    }
+                    else
+                    {
+                        if ($configs{"BoxColor"}) {
+                            $curr_graphics->setAttribute("FillColor",$configs{"BoxColor"}); }
+                    }
     
                     if ($is_first_homolog) 
                     {
@@ -813,7 +831,6 @@ init;
 
 import_data;
 show_input;
-exit
 swap_genes();
 show_output;
 export_data;