iroki 0.0.35 → 0.0.36

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 62543daefa15a5d64a7d9b48e738bf921da3be9f
-  data.tar.gz: e6278b2097ee763d828a43d21d95c85cc68776f4
+  metadata.gz: cc9840c73024ff89c424b094e52f70b474d1ffa1
+  data.tar.gz: 9c6cbea037206118e5e2bd3174b3553f0a00df2d
 SHA512:
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-  data.tar.gz: bcd3517d8cc582d6c97929374ec1c129e52f3fae550287d9ee697626a87fc3a6bb51b68b335e02227c665c57599db541598a3efc19d92e09804f157366cb3f67
+  metadata.gz: e278234fdd472f4ce6452701d2c1151b7a433df70081eaaf867b7011a64edfd5ef306061ea94c7c9526d2d2892b3f2ca317f1341e56216d5ccfd107992d55915
+  data.tar.gz: a621bf4408197fa5db28c28b51b8c12a13284e2328a28e39cdb8ed81a46544c8d879a5b009f39235158cd2eac575c40b5d5fa22536cbb216a777ffb2ed81adf2

data/exe/iroki

@@ -39,9 +39,9 @@ opts = Trollop.options do
       "Color branches?",
       short: "-b")
 
-  opt(:color_taxa_names,
+  opt(:color_labels,
       "Color label names?",
-      short: "-t")
+      short: "-l")
 
   opt(:exact,
       "Exact pattern matching")
@@ -99,7 +99,7 @@ end
 
 Iroki::Main.main(
   color_branches:             opts[:color_branches],
-  color_taxa_names:           opts[:color_taxa_names],
+  color_taxa_names:           opts[:color_labels],
   exact:                      opts[:exact],
   remove_bootstraps_below:    opts[:remove_bootstraps_below],
   color_map_f:                opts[:color_map],

data/lib/iroki/biom.rb

@@ -49,7 +49,8 @@ module Iroki
             first_line_count = the_counts.count
           else
             abort_unless first_line_count == the_counts.count,
-                         "Line number #{idx+1} (#{line.inspect}) in the " +
+                         "Line number #{idx+1} (#{line.inspect}) " +
+                         "in the " +
                          "biom file has #{the_counts.count} " +
                          "columns when it should have " +
                          "#{first_line_count} columns like the " +

data/lib/iroki/color/color.rb

@@ -725,8 +725,16 @@ module Iroki
         colors = COLORS
       end
 
-      abort_unless colors.has_key?(col),
-                   "Color '#{col}' is not defined."
+      unless colors.has_key? col
+        if col.match(/\A[0-9]+\Z/)
+          msg = "Color '#{col}' is not defined. " +
+                "Did you forget the --auto-color option?"
+        else
+          msg = "Color '#{col}' is not defined."
+        end
+
+        abort_if true, msg
+      end
 
       hex = colors[col]
       %Q{[&!color="#{hex.upcase}"]}

data/lib/iroki/color/gradient.rb

@@ -55,7 +55,7 @@ module Iroki
         old_min = old_min.to_f
         old_max = old_max.to_f
 
-(new_max - ((((new_max - new_min) * (x - old_min.to_f)) / (old_max - old_min)) + new_min)) + new_min
+        (new_max - ((((new_max - new_min) * (x - old_min.to_f)) / (old_max - old_min)) + new_min)) + new_min
       end
 
       def patterns

data/lib/iroki/color/palette/palette.rb

@@ -1,18 +1,6 @@
 module Iroki
   module Color
     module Palette
-      # BASIC =
-      #   { "1" => "#FF3814",   # red
-      #     "2" => "#712BFF",   # blue
-      #     "3" => "#FFDF14",   # yellow
-      #     "4" => "#14FF63", } # green
-
-      # FUNKY =
-      #   { "1" => "#FF7314",
-      #     "2" => "#9F23FF",
-      #     "3" => "#FFF814",
-      #     "4" => "#14FFD8", }
-
       KELLY = {
         "1"  => { name: "purple",          hex: "#875692" },
         "2"  => { name: "orange",          hex: "#F38400" },

data/lib/iroki/color/single_group_gradient.rb

@@ -53,8 +53,6 @@ module Iroki
 
           col =
             Iroki::Color::GREEN.mix_with Iroki::Color::BLUE, rel_abund
-          # col =
-          #   Iroki::Color::BLUE.mix_with Iroki::Color::GREEN, rel_abund
 
           col.luminosity = lumin
 
@@ -65,7 +63,6 @@ module Iroki
       def single_color_gradient_hex_codes
         @rel_abunds.zip(@lumins).map do |rel_abund, lumin|
           amt_of_orig_color =
-            # scale rel_abund, new_min=10, new_max=95
             scale rel_abund, new_min=@min_lumin, new_max=@max_lumin
 
           col =

data/lib/iroki/const/const.rb

@@ -18,17 +18,6 @@
 
 module Iroki
   module Const
-    COPYRIGHT = "2016 Ryan Moore"
-    CONTACT   = "moorer@udel.edu"
-    WEBSITE   = "https://github.com/mooreryan/color_tree"
-    LICENSE   = "GPLv3"
-
-    VERSION_BANNER = "  # Version: #{Iroki::VERSION}
-  # Copyright #{COPYRIGHT}
-  # Contact: #{CONTACT}
-  # Website: #{WEBSITE}
-  # License: #{LICENSE}"
-
     FIG = 'begin figtree;
 	set appearance.backgroundColorAttribute="Default";
 	set appearance.backgroundColour=#-1;

data/lib/iroki/core_ext/file/file.rb

@@ -21,14 +21,14 @@ def color_given? str
 end
 
 # TODO spec this for hex matching
-def has_label_tag? str
+def label_tag? str
   m = str.match(/\Alabel:(#?\p{Alnum}+)\Z/i)
 
   m[1] if m
 end
 
 # TODO spec this for hex matching
-def has_branch_tag? str
+def branch_tag? str
   m = str.match(/\Abranch:(#?\p{Alnum}+)\Z/i)
 
   m[1] if m
@@ -60,87 +60,8 @@ module Iroki
         arg
       end
 
-      # TODO this is now pointless
-      def parse_color_map fname,
-                          exact_matching: true,
-                          auto_color: false
-
-        check_file fname, :color_map
-
-
-        patterns = {}
-        Object::File.open(fname, "rt").each_line do |line|
-          unless line.start_with? "#"
-            label_tag = ""
-            branch_tag = ""
-
-            pattern, label_color, branch_color = line.chomp.split "\t"
-
-            # color = "black" if color.nil? || color.empty?
-
-            assert pattern, "found no pattern"
-
-            if exact_matching # TODO should this really be everytime?
-              pattern = pattern#.clean_name
-            else
-              # TODO flag bad regexp
-              pattern = Regexp.new pattern
-            end
-
-            if color_given?(label_color) && color_given?(branch_color)
-              abort_if(has_label_tag?(label_color) &&
-                       has_label_tag?(branch_color),
-                       "Label tag specified twice for '#{line}'")
-
-              abort_if(has_branch_tag?(label_color) &&
-                       has_branch_tag?(branch_color),
-                       "Branch tag specified twice for '#{line}'")
-            end
-
-            if color_given?(label_color) && !color_given?(branch_color)
-              if (color = has_label_tag? label_color)
-                label_tag = Iroki::Color.get_tag color, auto_color
-              elsif (color = has_branch_tag? label_color)
-                branch_tag = Iroki::Color.get_tag color, auto_color
-              else
-                label_tag = Iroki::Color.get_tag label_color, auto_color
-                branch_tag = Iroki::Color.get_tag label_color, auto_color
-              end
-            else
-              if color_given? label_color
-                if (color = has_label_tag? label_color)
-                  label_tag = Iroki::Color.get_tag color, auto_color
-                elsif (color = has_branch_tag? label_color)
-                  branch_tag = Iroki::Color.get_tag color, auto_color
-                else
-                  label_tag = Iroki::Color.get_tag label_color, auto_color
-                end
-              end
-
-              if color_given? branch_color
-                if (color = has_branch_tag? branch_color)
-                  branch_tag = Iroki::Color.get_tag color, auto_color
-                elsif (color = has_label_tag? branch_color)
-                  label_tag = Iroki::Color.get_tag color, auto_color
-                else
-                  branch_tag = Iroki::Color.get_tag branch_color, auto_color
-                end
-              end
-            end
-
-            # if auto_color
-            #   patterns[pattern] = "[&!color=\"#{auto_colors[color]}\"]"
-            # else
-            #   patterns[pattern] = Iroki::Color.get_tag color, auto_color
-            # end
-
-            patterns[pattern] = { label: label_tag, branch: branch_tag }
-          end
-        end
-
-        patterns
-      end
-
+      # TODO what's the point of the iroki_to_name? To allow wonky
+      # chars maybe?
       def parse_color_map_iroki(fname,
                                 iroki_to_name,
                                 exact_matching: true,
@@ -168,7 +89,6 @@ module Iroki
             assert pattern, "found no pattern"
 
             if exact_matching # TODO should this really be everytime?
-            # pattern = pattern.clean_name
               if name_to_iroki.has_key? pattern
                 pattern = name_to_iroki[pattern]
               else
@@ -181,56 +101,72 @@ module Iroki
               pattern = Regexp.new pattern
             end
 
-            if color_given?(label_color) && color_given?(branch_color)
-              abort_if(has_label_tag?(label_color) &&
-                       has_label_tag?(branch_color),
-                       "Label tag specified twice for '#{line}'")
 
-              abort_if(has_branch_tag?(label_color) &&
-                       has_branch_tag?(branch_color),
-                       "Branch tag specified twice for '#{line}'")
+            if color_given?(label_color) && color_given?(branch_color)
+              if label_tag?(label_color) &&
+                 label_tag?(branch_color)
+
+                abort_unless label_color == branch_color,
+                             "Label tags specified twice for " +
+                             "#{line.inspect}, but the tags don't " +
+                             "match."
+
+                # ie both are label tags specifying the same color
+                branch_color = nil
+              elsif branch_tag?(label_color) &&
+                    branch_tag?(branch_color)
+
+                abort_unless label_color == branch_color,
+                             "Branch tags specified twice for " +
+                             "#{line.inspect}, but the tags don't " +
+                             "match."
+
+                # ie both are branch tags specifying the same color
+                label_color = nil
+              end
             end
 
             if color_given?(label_color) && !color_given?(branch_color)
-              if (color = has_label_tag? label_color)
+              if (color = label_tag? label_color)
                 label_tag = Iroki::Color.get_tag color, auto_color
-              elsif (color = has_branch_tag? label_color)
+              elsif (color = branch_tag? label_color)
                 branch_tag = Iroki::Color.get_tag color, auto_color
-              elsif line.match(/\t\Z/) # empty branch color, branch will be black
-                label_tag = Iroki::Color.get_tag label_color, auto_color
+              elsif line.match(/\t\Z/) # empty branch color, branch
+                                       # will be black
+                label_tag = Iroki::Color.get_tag label_color,
+                                                 auto_color
               else
-                label_tag = Iroki::Color.get_tag label_color, auto_color
-                branch_tag = Iroki::Color.get_tag label_color, auto_color
+                label_tag = Iroki::Color.get_tag label_color,
+                                                 auto_color
+                branch_tag = Iroki::Color.get_tag label_color,
+                                                  auto_color
               end
             else
               if color_given? label_color
-                if (color = has_label_tag? label_color)
+                if (color = label_tag? label_color)
                   label_tag = Iroki::Color.get_tag color, auto_color
-                elsif (color = has_branch_tag? label_color)
+                elsif (color = branch_tag? label_color)
                   branch_tag = Iroki::Color.get_tag color, auto_color
                 else
-                  label_tag = Iroki::Color.get_tag label_color, auto_color
+                  label_tag = Iroki::Color.get_tag label_color,
+                                                   auto_color
                 end
               end
 
               if color_given? branch_color
-                if (color = has_branch_tag? branch_color)
+                if (color = branch_tag? branch_color)
                   branch_tag = Iroki::Color.get_tag color, auto_color
-                elsif (color = has_label_tag? branch_color)
+                elsif (color = label_tag? branch_color)
                   label_tag = Iroki::Color.get_tag color, auto_color
                 else
-                  branch_tag = Iroki::Color.get_tag branch_color, auto_color
+                  branch_tag = Iroki::Color.get_tag branch_color,
+                                                    auto_color
                 end
               end
             end
 
-            # if auto_color
-            #   patterns[pattern] = "[&!color=\"#{auto_colors[color]}\"]"
-            # else
-            #   patterns[pattern] = Iroki::Color.get_tag color, auto_color
-            # end
-
-            patterns[pattern] = { label: label_tag, branch: branch_tag }
+            patterns[pattern] = { label: label_tag,
+                                  branch: branch_tag }
           end
         end
 
@@ -258,9 +194,6 @@ module Iroki
             abort_if newname.nil? || newname.empty?,
                      "Column 2 missing for line: #{line.inspect}"
 
-            # oldname = oldname.clean_name
-            # newname = newname.clean_name
-
             abort_if name_map.has_key?(oldname),
                      "#{oldname} is repeated in column 1"
 

data/lib/iroki/core_ext/string/string.rb

@@ -12,16 +12,13 @@ module Iroki
       end
 
       def clean
-        # puts %Q{clean: #{self}, #{self.gsub(/'/, '"')}}
         self.gsub(/'/, '"')
       end
 
       def single_quote
         if self.match /\A'.*'\Z/
-          # puts %Q{single_quote if: #{self}, outputing #{self.dup}}
           self.dup
         else
-          # puts %Q{single_quote else: #{self}, returning '#{self.clean}'}
           %Q['#{self.clean}']
         end
       end
@@ -31,11 +28,8 @@ module Iroki
           name = match[1]
           color = match[2]
 
-          # puts %Q{clean_name if: #{self}, returning #{name.single_quote + color}}
           name.single_quote + color
-          # name + color
         else
-          # puts %Q{clean_name else: #{self}, returning #{self.single_quote}}
           self.single_quote
         end
       end
@@ -44,11 +38,9 @@ module Iroki
         self.strip.gsub(/[^\p{Alnum}_]+/, "_").gsub(/_+/, "_")
       end
 
-
       def has_single_quote?
         self.match(/'/)
       end
-
     end
   end
 end

data/lib/iroki/main/main.rb

@@ -261,6 +261,19 @@ module Iroki
       # newick = treeio.next_entry
       str = File.read newick
       newick = Bio::Newick.new str, parser: :iroki
+
+      # Warn if there is extra info in the newick file
+      if newick &&
+         newick.entry_overrun &&
+         !newick.entry_overrun.chomp.empty?
+
+        AbortIf.logger.warn {
+          "Extra info (#{newick.entry_overrun}) in newick file " +
+            "(#{newick_f}) will be ignored. " +
+            "Does your newick file contain multiple trees?"
+        }
+      end
+
       tree = newick.tree
 
       # puts [:tree_first_parsed, tree.newick(indent: false)]

data/lib/iroki/tree.rb

@@ -15,6 +15,9 @@ module Iroki
     # @param [Bio::Tree] a bio ruby tree object
     #
     # @return [Hash] iroki_name (string) => quoted_orig_name (string)
+    #
+    # @todo not a good name as it doesn't actually change the names in
+    #   the tree
     def self.change_names tree
       idx = -1
       realname = {}
@@ -50,12 +53,15 @@ module Iroki
       hash.values.map(&:single_quote)
     end
 
-    def self.gsub_iroki_newick_string tre_str, iroki_to_name, name_map=nil
+    def self.gsub_iroki_newick_string tre_str,
+                                      iroki_to_name,
+                                      name_map=nil
       if name_map
         vals = self.quoted_vals name_map
         name_map_quoted = Hash[name_map.keys.zip(vals)]
 
-        iroki_to_new_name = self.combine_hashes iroki_to_name, name_map_quoted
+        iroki_to_new_name =
+          self.combine_hashes iroki_to_name, name_map_quoted
       else
         vals = self.quoted_vals iroki_to_name
 
@@ -65,22 +71,33 @@ module Iroki
       tre_str.gsub(/iroki[0-9]+iroki/, iroki_to_new_name)
     end
 
-    def self.iroki_to_color iroki_to_name, color_map, name_map, nil_val=nil
+    def self.iroki_to_color iroki_to_name,
+                            color_map,
+                            name_map,
+                            nil_val=nil
       if name_map
         old_names = name_map.keys
         new_names = name_map.values
 
-        color_map_is_for_old_names = color_map.keys.all? { |key| old_names.include? key }
-        color_map_is_for_new_names = color_map.keys.all? { |key| new_names.include? key }
+        color_map_is_for_old_names =
+          color_map.keys.all? { |key| old_names.include? key }
+
+        color_map_is_for_new_names =
+          color_map.keys.all? { |key| new_names.include? key }
 
         if color_map_is_for_old_names
-          iroki_to_color = self.combine_hashes iroki_to_name, color_map, nil_val
+          iroki_to_color =
+            self.combine_hashes iroki_to_name, color_map, nil_val
         elsif color_map_is_for_new_names
-          iroki_to_new_name = self.combine_hashes iroki_to_name, name_map
+          iroki_to_new_name =
+            self.combine_hashes iroki_to_name, name_map
 
-          iroki_to_color = self.combine_hashes iroki_to_new_name, color_map, nil_val
+          iroki_to_color =
+            self.combine_hashes iroki_to_new_name, color_map, nil_val
         else # some old, some new
-          abort_if true, "The color map has both old and new names in the first column."
+          abort_if true,
+                   "The color map has both old and new names in " +
+                   "the first column."
         end
 
         iroki_to_color

data/lib/iroki/utils/utils.rb

@@ -42,16 +42,21 @@ module Iroki
         end
       else
         assert iroki_to_name, "iroki_to_name arg is nil"
-        assert iroki_to_name[node.to_s], "iroki_to_name is missing #{node.to_s}"
+        assert iroki_to_name[node.to_s],
+               "iroki_to_name is missing #{node.to_s}"
         node_s = iroki_to_name[node.to_s]
 
         patterns.each do |pattern, this_color|
           if node_s =~ pattern
             abort_if already_matched,
-                     "Non specific matching for #{node_s}"
+                     "Non specific matching for #{node_s}. " +
+                     "Previously matched pattern was " +
+                     "#{already_matched.inspect}. Current pattern " +
+                     "is " +
+                     "#{pattern.inspect}. Color was #{this_color}."
 
             color = this_color
-            already_matched = true
+            already_matched = pattern
           end
         end
 
@@ -93,7 +98,10 @@ module Iroki
 
         # NOTE: this was originally before cleaning the node name a
         # couple lines up, does it matter that it is after?
-        color = add_color_to_leaf_branch patterns, node, exact, iroki_to_name
+        color = add_color_to_leaf_branch patterns,
+                                         node,
+                                         exact,
+                                         iroki_to_name
 
         # add color to the name
         node.name = node.name + color[:branch] if color

data/lib/iroki/version.rb

@@ -18,7 +18,7 @@
 
 # Library metadata
 module Iroki
-  VERSION = "0.0.35"
+  VERSION = "0.0.36"
   COPYRIGHT = "2015 - 2017 Ryan Moore"
   CONTACT   = "moorer@udel.edu"
   WEBSITE   = "https://github.com/mooreryan/iroki"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: iroki
 version: !ruby/object:Gem::Version
-  version: 0.0.35
+  version: 0.0.36
 platform: ruby
 authors:
 - Ryan Moore
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2017-05-14 00:00:00.000000000 Z
+date: 2017-07-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler