From eaa7cb81a4ae7bb1dc9c7629d7365131db22ffef Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 10 Oct 2012 12:28:52 +0000
Subject: [PATCH] removed stale file crap from biostat

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1959 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/biostat           |  5 -----
 bp_bin/classify_taxonomy | 13 ++++++++++++-
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/bp_bin/biostat b/bp_bin/biostat
index 6a7d040..d409d28 100755
--- a/bp_bin/biostat
+++ b/bp_bin/biostat
@@ -76,11 +76,6 @@ while ( 1 )
 
             push @table, $info;
         }
-        else
-        {
-            print STDERR "Removing stale file: $file\n";
-            unlink $file;
-        }
     }
 
     if ( $options->{ 'sort' } =~ /^(USER|TMP_DIR|START_TIME|RUN_TIME|COMMAND)$/ ) {
diff --git a/bp_bin/classify_taxonomy b/bp_bin/classify_taxonomy
index 1614e5d..8c211de 100755
--- a/bp_bin/classify_taxonomy
+++ b/bp_bin/classify_taxonomy
@@ -31,7 +31,10 @@
 require 'pp'
 require 'maasha/biopieces'
 
+# Class containing methods to construct a taxonomic tree for the classification of
+# organisms. Currently only works with GreenGenes type of entries.
 class TaxTree
+  # Method to initialize a new TaxTree object.
   def initialize
     @tree = TaxNode.new("root", "Root", 0, 0, 0.0)
   end
@@ -55,6 +58,7 @@ class TaxTree
     end
   end
 
+  # Method to merge two TaxTrees.
   def merge(tree)
     node = @tree
 
@@ -76,6 +80,7 @@ class TaxTree
     end
   end
 
+  # Method to flatten a TaxTree turning this into a list by recursive depth first traversal.
   def flatten(node = @tree, list = [])
     list << TaxNode.new(node.level, node.name, node.count, node.size, node.score)
 
@@ -86,6 +91,8 @@ class TaxTree
     list
   end
 
+  # Method to recursively trim a TaxTree show that it only contains a unbranched tree,
+  # which gives the lowest common ancestor.
   def lowest_common_ancestor(node = @tree)
     node.children = {} if node.children.size > 1
 
@@ -94,6 +101,7 @@ class TaxTree
     end
   end
 
+  # Method for iterating over a TaxTree.
   def each
     self.flatten.each do |node|
       yield node
@@ -104,6 +112,7 @@ class TaxTree
 
   private
 
+  # Method containing a helper hash to expand the phylogenetic level name.
   def expand_level(level)
     hash = {
       'd' => "domain",
@@ -121,6 +130,7 @@ class TaxTree
     hash[level]
   end
 
+  # Nested class for TaxTree nodes.
   class TaxNode
     attr_accessor :level, :name, :count, :size, :score, :children
 
@@ -133,6 +143,7 @@ class TaxTree
       @children = {}
     end
 
+    # Method to convert a TaxNode to a Biopiece record.
     def to_bp
       record = {}
       record[:REC_TYPE] = "Classification"
@@ -148,7 +159,7 @@ end
 
 casts = []
 casts << {:long=>'LCA',  :short=>'l', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'size', :short=>'s', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'size', :short=>'s', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
 
 options = Biopieces.options_parse(ARGV, casts)
 
-- 
2.39.5