Changed refs from "paralog" to "homolog"; edited perldoc

svn path=/; revision=151

diff --git a/preecej/perl_singletons/pathway_gene_swapper.pl b/preecej/perl_singletons/pathway_gene_swapper.pl
index 1e05a4949dea6887bf6533ef5d51f49a3f926667..c01ec1bac2213117d97262a6abb25d1f0d8dcf5b 100644 (file)
--- a/preecej/perl_singletons/pathway_gene_swapper.pl
+++ b/preecej/perl_singletons/pathway_gene_swapper.pl
@@ -10,8 +10,8 @@ Pathway Gene Swapper
 
 =head1 DESCRIPTION
 
-Swap out one set of genes for another in an existing PathVisio GPML
-file. Optionally removes literature references.
+Swap out one set of genes (or gene representation) for another in an 
+existing PathVisio GPML file. Optionally removes literature references.
 
 If multiple replacement genes map to a single original gene,
 multiple PathVisio boxes will be drawn in place of the 
@@ -56,8 +56,8 @@ pathway_gene_swapper.pl -i INPUT_FILE -g GENE_FILE -c CONFIG_FILE -o OUTPUT_FILE
         The first column must have one and only one gene -- the 
         "original" gene.
         
-        The second column may have one and only one gene variants or 
-        paralog -- the "replacement" gene(s).
+        The second column may have one and only one gene variant or 
+        homolog -- the "replacement" gene(s).
     
     - The config file may have any or all of the following entries,
       in addition to the required fields (in any order):
@@ -282,7 +282,7 @@ sub import_data
     
     # used to generate total counts of each species' gene list; sanity check
     my $original_gene_count = 0;
-    my $replacement_paralog_count = 0;
+    my $replacement_homolog_count = 0;
 
     my $line = <GENE_FILE>;
     
@@ -299,19 +299,19 @@ sub import_data
        {
            $original_gene_count++;
        }
-       $replacement_paralog_count++; # count this every time
+       $replacement_homolog_count++; # count this every time
        
        # add new gene to hash value (array) for old gene hash key
        push @{$swap_genes{$data_field}},$data_val;      
     } 
     
-    if ($verbose) # give add'l stats on gene and paralog counts
+    if ($verbose) # give add'l stats on gene and homolog counts
     {
-        print "[Total number of original genes and paralogs]\n"
+        print "[Total number of original genes and homologs]\n"
             . "Original gene count: " . $original_gene_count . "\n"
-            . "Replacement paralog count: $replacement_paralog_count\n\n"; 
+            . "Replacement homolog count: $replacement_homolog_count\n\n"; 
     
-        print "[Number of paralogs per original gene]\n";
+        print "[Number of homologs per original gene]\n";
         foreach my $orig_gene_key (keys %swap_genes)
         {
             print "$orig_gene_key: " . scalar(@{$swap_genes{$orig_gene_key}}) . "\n";
@@ -367,7 +367,7 @@ Returns a string containing the new hex id.
 sub create_unique_hex_id($$)
 {
     # NOTE: This algorithm breaks down at VERY large scale (100K genes+). The
-    # larger the number of original genes, groups, and new paralogs you need to
+    # larger the number of original genes, groups, and new homologs you need to
     # create, the more inefficient it becomes to make sure your "random" 5-digit
     # hex number is not already present in your "existing ids" list via 
     # recursion. However, for a few hundred or thousand genes, it should be ok.
@@ -532,7 +532,7 @@ sub swap_genes
             }
             # print "@new_nodes_map\n"; # TEST
 
-            # if more than one new paralog exists, and the old gene doesn't
+            # if more than one new homolog exists, and the old gene doesn't
             # already belong to a group, you'll need a new Group for multiple 
             # gene boxes
             my $new_GroupId;
@@ -566,8 +566,8 @@ sub swap_genes
                 }
             }
             
-            # flag for determining if there are one or many replacement paralogs
-            my $is_first_paralog = 1; 
+            # flag for determining if there are one or many replacement homologs
+            my $is_first_homolog = 1; 
 
             # makes sure each box is increasingly offset from the original
             # (in all three dimensions)
@@ -583,14 +583,14 @@ sub swap_genes
                 }
                 
                 my $curr_new_node = $$_[0];
-                my $curr_paralog = $$_[1];
-                # print "$_: $curr_new_node, $curr_paralog\n"; # TEST
+                my $curr_homolog = $$_[1];
+                # print "$_: $curr_new_node, $curr_homolog\n"; # TEST
                 # print "[Curr New Node before editing...]\n" . $curr_new_node->toString . "\n\n"; # TEST
                 
                 # update all new nodes w/ attributes...
 
                 # rename TextLabel...
-                # prefix (from config), suffix: new '-#' for multiple paralogs
+                # prefix (from config), suffix: new '-#' for multiple homologs
                 $curr_new_node->setAttribute("TextLabel",
                     (($configs{"LabelPrefix"}) ? $configs{"LabelPrefix"} : "")
                         . $curr_new_node->getAttributeNode("TextLabel")->getValue
@@ -606,13 +606,13 @@ 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.");
                 $curr_new_node->insertBefore($new_comment,$curr_new_node->getFirstChild); # assumes other child nodes  
                 
                 # edit <Xref Database="JGI" ID="Egrandis..." />
                 my $curr_xref = ($curr_new_node->getElementsByTagName("Xref"))[0];
                 $curr_xref->setAttribute("Database",$configs{"Database"});
-                $curr_xref->setAttribute("ID",$curr_paralog);
+                $curr_xref->setAttribute("ID",$curr_homolog);
 
                 # change box width and colors (<Graphics...Color="4488ff" ... />)
                 my $curr_graphics = ($curr_new_node->getElementsByTagName("Graphics"))[0];
@@ -622,16 +622,16 @@ sub swap_genes
                 if ($configs{"BoxColor"}) {
                     $curr_graphics->setAttribute("FillColor",$configs{"BoxColor"}); }
 
-                if ($is_first_paralog) 
+                if ($is_first_homolog) 
                 {
-                    # print "that was the first paralog...\n"; # TEST
-                    $is_first_paralog = 0; # first paralog complete
+                    # print "that was the first homolog...\n"; # TEST
+                    $is_first_homolog = 0; # first homolog complete
                 }
-                else # add'l paralogs required
+                else # add'l homologs required
                 {
                     $offset_multiplier++;
                     
-                    # print "that was an add'l paralog, change more attrs...\n"; # TEST
+                    # print "that was an add'l homolog, change more attrs...\n"; # TEST
                     # update add'l nodes w/ special attributes...
 
                     # generate a new DataNode GraphId not already in use