egor 0.0.3 → 0.0.4

data/History.txt

@@ -1,3 +1,9 @@
+== 0.0.4 2008-12-15
+
+* 2 major enhancement:
+  * log-odds ratio matrices can be generated with --nosmooth option
+  * safe handling for zero observations or mutations of amino acids
+
 == 0.0.3 2008-12-09
 
 * 2 major enhancement:

data/README.rdoc

@@ -65,7 +65,7 @@ egor: Esst GeneratOR, a program for calculating environment-specific substitutio
 
 == REQUIREMENTS:
 
-* ruby 1.8.6 or above (http://www.ruby-lang.org)
+* ruby 1.8.7 or above (http://www.ruby-lang.org)
 * rubygems 1.2.0 or above (http://rubyforge.org/projects/rubygems/)
 
 Following RubyGems will be automatically installed if you have rubygems installed on your machine

data/egor.gemspec

@@ -2,12 +2,12 @@
 
 Gem::Specification.new do |s|
   s.name = %q{egor}
-  s.version = "0.0.3"
+  s.version = "0.0.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Semin Lee"]
   s.cert_chain = ["/Users/semin/.gem/gem-public_cert.pem"]
-  s.date = %q{2008-12-09}
+  s.date = %q{2008-12-15}
   s.default_executable = %q{egor}
   s.description = %q{egor: Esst GeneratOR, a program for calculating environment-specific substitution tables}
   s.email = ["seminlee@gmail.com"]
@@ -34,14 +34,14 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
       s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
       s.add_runtime_dependency(%q<simple_memoize>, [">= 1.0.0"])
-      s.add_development_dependency(%q<newgem>, [">= 1.1.0"])
+      s.add_development_dependency(%q<newgem>, [">= 1.2.1"])
       s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
     else
       s.add_dependency(%q<narray>, [">= 0.5.9.5"])
       s.add_dependency(%q<bio>, [">= 1.2.1"])
       s.add_dependency(%q<facets>, [">= 2.4.5"])
       s.add_dependency(%q<simple_memoize>, [">= 1.0.0"])
-      s.add_dependency(%q<newgem>, [">= 1.1.0"])
+      s.add_dependency(%q<newgem>, [">= 1.2.1"])
       s.add_dependency(%q<hoe>, [">= 1.8.0"])
     end
   else
@@ -49,7 +49,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<bio>, [">= 1.2.1"])
     s.add_dependency(%q<facets>, [">= 2.4.5"])
     s.add_dependency(%q<simple_memoize>, [">= 1.0.0"])
-    s.add_dependency(%q<newgem>, [">= 1.1.0"])
+    s.add_dependency(%q<newgem>, [">= 1.2.1"])
     s.add_dependency(%q<hoe>, [">= 1.8.0"])
   end
 end

data/lib/egor/cli.rb

@@ -48,13 +48,13 @@ Options:
     --weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting
     --noweight: calculate substitution counts with no weights (default)
     --smooth (-s) INTEGER:
-        0 for parial smoothing (default)
+        0 for partial smoothing (default)
         1 for full smoothing
     --nosmooth: perform no smoothing operation
     --cys (-y) INTEGER:
         0 for using C and J only for structure (default)
         1 for both structure and sequence
-        2 for using only C for both
+        2 for using only C for both (should be set having no 'disulphide bonds' environment feature)
     --output INTEGER:
         0 for raw counts (no-smoothing performed)
         1 for probabilities
@@ -163,6 +163,9 @@ Options:
         $tot_freq_mat = nil
         $tot_prob_mat = nil
         $tot_logo_mat = nil
+        #
+        # Part 1 END
+        #
 
         # Part 2.
         #
@@ -174,6 +177,7 @@ Options:
           [ '--tem-file', '-f', GetoptLong::REQUIRED_ARGUMENT ],
           [ '--classdef', '-c', GetoptLong::REQUIRED_ARGUMENT ],
           [ '--smooth',   '-s', GetoptLong::REQUIRED_ARGUMENT ],
+          [ '--nosmooth',       GetoptLong::NO_ARGUMENT ],
           [ '--weight',   '-w', GetoptLong::REQUIRED_ARGUMENT ],
           [ '--noweight',       GetoptLong::NO_ARGUMENT ],
           [ '--heatmap',        GetoptLong::NO_ARGUMENT ],
@@ -249,6 +253,9 @@ Options:
           print_usage
           exit 1
         end
+        #
+        # Part 2 END
+        #
 
 
         # Part 3.
@@ -315,6 +322,9 @@ Options:
         }.each_with_index { |e, i|
           $envs[e.flatten.join] = Environment.new(i, e.flatten.join, $amino_acids)
         }
+        #
+        # Part 3 END
+        #
 
         # Part 4.
         #
@@ -621,7 +631,7 @@ Options:
                 end
               end
             end
-          end # if !$nosmooth
+          end
         end
 
         # print out default header
@@ -660,7 +670,13 @@ HEADER
 
         # calculate amino acid frequencies and mutabilities, and
         # print them as default statistics in the header part
-        ala_factor  = 100.0 * $aa_tot_obs["A"] / $aa_mut_obs["A"].to_f
+        ala_factor  = if $aa_tot_obs["A"] == 0
+                        0.0
+                      elsif $aa_mut_obs["A"] == 0
+                        0.0
+                      else
+                        100.0 * $aa_tot_obs["A"] / $aa_mut_obs["A"].to_f
+                      end
         $tot_aa     = $aa_tot_obs.values.sum
 
         $outfh.puts "#"
@@ -668,9 +684,9 @@ HEADER
         $outfh.puts "# %-3s %9s %9s %5s %8s %8s" % %w[RES TOT_OBS MUT_OBS MUTB REL_MUTB REL_FRQ]
 
         $amino_acids.each do |res|
-          $aa_mutb[res]     = $aa_mut_obs[res] / $aa_tot_obs[res].to_f
+          $aa_mutb[res]     = $aa_tot_obs[res] == 0 ? 1.0 : $aa_mut_obs[res] / $aa_tot_obs[res].to_f
           $aa_rel_mutb[res] = $aa_mutb[res] * ala_factor
-          $aa_rel_freq[res] = $aa_tot_obs[res] / $tot_aa.to_f
+          $aa_rel_freq[res] = $aa_tot_obs[res] == 0 ? 0.0 : $aa_tot_obs[res] / $tot_aa.to_f
         end
 
         $amino_acids.each do |res|
@@ -682,6 +698,9 @@ HEADER
               [res, $aa_tot_obs[res], $aa_mut_obs[res], $aa_mutb[res], $aa_rel_mutb[res], $aa_rel_freq[res]]
           end
         end
+        #
+        # Part 4. END
+        #
 
 
         # Part 5.
@@ -728,6 +747,9 @@ HEADER
           $outfh.puts $tot_freq_mat.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids)
           exit 0
         end
+        #
+        # Part 5. END
+        #
 
 
         # Part 6.
@@ -746,6 +768,7 @@ HEADER
 HEADER
         end
 
+        # when nosmoothing !!!
         if ($output > 0) && $nosmooth
           # Probability matrices
           $tot_prob_mat = NMatrix.float($amino_acids.size, $amino_acids.size)
@@ -781,7 +804,7 @@ HEADER
           end
         end
 
-        # for smoothing...
+        # when smoothing!!!
         if ($output > 0) && !$nosmooth
           #
           # p1 probability
@@ -905,7 +928,13 @@ HEADER
 
                   # entropy based weighting priors
                   entropy_max     = Math::log($amino_acids.size)
-                  entropies       = priors.map { |prior| -1.0 * prior.to_a.inject(0.0) { |s, p| p == 0.0 ? s - 1 : s + p * Math::log(p) } }
+                  entropies       = priors.map { |prior| -1.0 * prior.to_a.inject(0.0) { |s, p|
+                    begin
+                      p == 0.0 ? s - 1 : s + p * Math::log(p)
+                    rescue
+                      #puts "P: #{p}"
+                    end
+                  } }
                   mod_entropies   = entropies.map_with_index { |entropy, i| (entropy_max - entropies[i]) / entropy_max }
                   weights         = mod_entropies.map { |mod_entropy| mod_entropy / mod_entropies.sum }
                   weighted_priors = priors.map_with_index { |prior, i| prior * weights[i] }.sum
@@ -1058,96 +1087,101 @@ HEADER
             $outfh.close
             exit 0
           end
+        end
+        #
+        # Part 6. END
+        #
 
 
-          # Part 7.
-          #
-          # Calculating log odds ratio scoring matrices
-          #
-          if $output == 2
-            $outfh.puts <<HEADER
+        # Part 7.
+        #
+        # Calculating log odds ratio scoring matrices
+        #
+        if $output == 2
+          $outfh.puts <<HEADER
 # 
 # The probabilities were then divided by the background probabilities
 HEADER
-            if $penv
-              $outfh.puts <<HEADER
+          if $penv
+            $outfh.puts <<HEADER
 # which were derived from the environment-independent amino acid frequencies.
 #                             ^^^^^^^^^^^^^^^^^^^^^^^
 HEADER
-            else
-              $outfh.puts <<HEADER
+          else
+            $outfh.puts <<HEADER
 # which were derived from the environment-dependent amino acid frequencies.
 #                             ^^^^^^^^^^^^^^^^^^^^^
 HEADER
-            end
+          end
 
-            $tot_logo_mat = $cys == 0 ? NMatrix.float($amino_acids.size, $amino_acids.size + 1) : NMatrix.float($amino_acids.size, $amino_acids.size)
-            grp_logo_mats = []
-            factor        = $scale / Math::log(2)
-
-            # grouping environments by its environment labels but amino acid label
-            env_groups = $envs.values.group_by { |env| env.label[1..-1] }
-
-            # sorting environments and build 21X21 substitution matrices
-            env_groups.to_a.sort_by { |env_group|
-              # a bit clumsy sorting here...
-              env_group[0].split("").map_with_index { |l, i|
-                $env_features[i + 1].labels.index(l)
-              }
-            }.each_with_index do |group, group_no|
-              # calculating 21X21 substitution probability matrix for each envrionment
-              grp_label     = group[0]
-              grp_envs      = group[1]
-              grp_logo_mat  = $cys == 0 ? NMatrix.float($amino_acids.size, $amino_acids.size + 1) : NMatrix.float($amino_acids.size, $amino_acids.size)
-
-              $amino_acids.each_with_index do |aa, ai|
-                env       = grp_envs.detect { |e| e.label.start_with?(aa) }
-                logo_arr  = $cys == 0 ? NArray.float($amino_acids.size + 1) : NArray.float($amino_acids.size)
-
-                env.smooth_prob_array.to_a.each_with_index do |prob, j|
-                  paj         = 100.0 * $aa_rel_freq[$amino_acids[j]]
-                  odds        = prob == 0.0 ? 0.000001 / paj : prob / paj
-                  logo_arr[j] = factor * Math::log(odds)
-                end
+          $tot_logo_mat = $cys == 0 ? NMatrix.float($amino_acids.size, $amino_acids.size + 1) : NMatrix.float($amino_acids.size, $amino_acids.size)
+          grp_logo_mats = []
+          factor        = $scale / Math::log(2)
+
+          # grouping environments by its environment labels but amino acid label
+          env_groups = $envs.values.group_by { |env| env.label[1..-1] }
+
+          # sorting environments and build 21X21 substitution matrices
+          env_groups.to_a.sort_by { |env_group|
+            # a bit clumsy sorting here...
+            env_group[0].split("").map_with_index { |l, i|
+              $env_features[i + 1].labels.index(l)
+            }
+          }.each_with_index do |group, group_no|
+            # calculating substitution probability matrix for each envrionment
+            grp_label     = group[0]
+            grp_envs      = group[1]
+            grp_logo_mat  = $cys == 0 ? NMatrix.float($amino_acids.size, $amino_acids.size + 1) : NMatrix.float($amino_acids.size, $amino_acids.size)
 
-                0.upto($amino_acids.size - 1) { |j| grp_logo_mat[ai, j] = logo_arr[j] }
+            $amino_acids.each_with_index do |aa, ai|
+              env       = grp_envs.detect { |e| e.label.start_with?(aa) }
+              logo_arr  = $cys == 0 ? NArray.float($amino_acids.size + 1) : NArray.float($amino_acids.size)
 
-                # adding log odds ratio for "U" (J or C) when --cyc is 0
-                if $cys == 0
-                  paj   = 100.0 * ($aa_rel_freq["C"] + $aa_rel_freq["J"])
-                  prob  = env.smooth_prob_array[$amino_acids.index("C")] + env.smooth_prob_array[$amino_acids.index("J")]
-                  odds  = prob == 0.0 ? 0.000001 / paj : prob / paj
-                  logo_arr[logo_arr.size - 1] = factor * Math::log(odds)
-                  grp_logo_mat[ai, logo_arr.size - 1] = logo_arr[logo_arr.size - 1]
-                end
+              env.send($nosmooth ? "prob_array" : "smooth_prob_array").to_a.each_with_index do |prob, j|
+                paj         = 100.0 * $aa_rel_freq[$amino_acids[j]]
+                odds        = prob == 0.0 ? 0.000001 / paj : prob / paj
+                logo_arr[j] = factor * Math::log(odds)
               end
 
-              $tot_logo_mat += grp_logo_mat
-              grp_logo_mats << [grp_label, grp_logo_mat]
+              0.upto($amino_acids.size - 1) { |j| grp_logo_mat[ai, j] = logo_arr[j] }
+
+              # adding log odds ratio for "U" (J or C) when --cyc is 0
+              if $cys == 0
+                paj   = 100.0 * ($aa_rel_freq["C"] + $aa_rel_freq["J"])
+                prob  = env.send($nosmooth ? "prob_array" : "smooth_prob_array")[$amino_acids.index("C")] +
+                        env.send($nosmooth ? "prob_array" : "smooth_prob_array")[$amino_acids.index("J")]
+                odds  = prob == 0.0 ? 0.000001 / paj : prob / paj
+                logo_arr[logo_arr.size - 1] = factor * Math::log(odds)
+                grp_logo_mat[ai, logo_arr.size - 1] = logo_arr[logo_arr.size - 1]
+              end
             end
 
-            $tot_logo_mat /= env_groups.size
-
-            # calculating relative entropy for each amino acid pair H and
-            # the expected score E in bit units
-            #
-            # I'm a bit suspicious about this part...
-            tot_E = 0.0
-            tot_H = 0.0
-
-            0.upto($tot_logo_mat.shape[0] - 1) do |i|
-              0.upto($tot_logo_mat.shape[0] - 1) do |j|
-                if i != j
-                  tot_E += $tot_logo_mat[i, j] * $aa_rel_freq[$amino_acids[i]] * $aa_rel_freq[$amino_acids[j]] / 2.0
-                  tot_H += $tot_logo_mat[i, j] * $tot_prob_mat[i, j] / 2.0 / 10000.0
-                else
-                  tot_E += $tot_logo_mat[i, j] * $aa_rel_freq[$amino_acids[i]] * $aa_rel_freq[$amino_acids[j]]
-                  tot_H += $tot_logo_mat[i, j] * $tot_prob_mat[i, j] / 10000.0
-                end
+            $tot_logo_mat += grp_logo_mat
+            grp_logo_mats << [grp_label, grp_logo_mat]
+          end
+
+          $tot_logo_mat /= env_groups.size
+
+          # calculating relative entropy for each amino acid pair H and
+          # the expected score E in bit units
+          #
+          # I'm a bit suspicious about this part...
+          tot_E = 0.0
+          tot_H = 0.0
+
+          0.upto($tot_logo_mat.shape[0] - 1) do |i|
+            0.upto($tot_logo_mat.shape[0] - 1) do |j|
+              if i != j
+                tot_E += $tot_logo_mat[i, j] * $aa_rel_freq[$amino_acids[i]] * $aa_rel_freq[$amino_acids[j]] / 2.0
+                tot_H += $tot_logo_mat[i, j] * $tot_prob_mat[i, j] / 2.0 / 10000.0
+              else
+                tot_E += $tot_logo_mat[i, j] * $aa_rel_freq[$amino_acids[i]] * $aa_rel_freq[$amino_acids[j]]
+                tot_H += $tot_logo_mat[i, j] * $tot_prob_mat[i, j] / 10000.0
               end
             end
+          end
 
-            $outfh.puts <<HEADER
+          $outfh.puts <<HEADER
 # 
 # Shown here are logarithms of these values multiplied by #{$scale}/log(2) 
 # rounded to the nearest integer (log-odds scores in 1/3 bit units).
@@ -1156,31 +1190,30 @@ HEADER
 #
 HEADER
 
-            grp_logo_mats.each_with_index do |arr, grp_no|
-              grp_label     = arr[0]
-              grp_logo_mat  = arr[1]
+          grp_logo_mats.each_with_index do |arr, grp_no|
+            grp_label     = arr[0]
+            grp_logo_mat  = arr[1]
 
-              $outfh.puts ">#{grp_label} #{grp_no}"
-              if $cys
-                $outfh.puts grp_logo_mat.round.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids + %w[U])
-              else
-                $outfh.puts grp_logo_mat.round.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids)
-              end
+            $outfh.puts ">#{grp_label} #{grp_no}"
+            if $cys
+              $outfh.puts grp_logo_mat.round.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids + %w[U])
+            else
+              $outfh.puts grp_logo_mat.round.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids)
             end
+          end
 
-            $outfh.puts ">Total #{grp_logo_mats.size}"
+          $outfh.puts ">Total #{grp_logo_mats.size}"
 
-            if $cys == 0
-              $outfh.puts $tot_logo_mat.round.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids + %w[U])
-            else
-              $outfh.puts $tot_logo_mat.round.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids)
-            end
-            $outfh.close
-            exit 0
+          if $cys == 0
+            $outfh.puts $tot_logo_mat.round.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids + %w[U])
+          else
+            $outfh.puts $tot_logo_mat.round.pretty_string(:col_header => $amino_acids, :row_header => $amino_acids)
           end
+          $outfh.close
+          exit 0
         end
       end
+    end
 
-    end # class << self
   end # class CLI
 end # module Egor

data/lib/egor.rb

@@ -2,5 +2,5 @@ $:.unshift(File.dirname(__FILE__)) unless
   $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
 
 module Egor
-  VERSION = '0.0.3'
+  VERSION = '0.0.4'
 end

data/website/index.html

@@ -34,7 +34,7 @@
     <div class="sidebar">
       <div id="version" class="clickable" onclick='document.location = "http://rubyforge.org/projects/egor"; return false'>
         <p>Get Version</p>
-        <a href="http://rubyforge.org/projects/egor" class="numbers">0.0.3</a>
+        <a href="http://rubyforge.org/projects/egor" class="numbers">0.0.4</a>
       </div>
     </div>
     <h2>What</h2>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: egor
 version: !ruby/object:Gem::Version 
-  version: 0.0.3
+  version: 0.0.4
 platform: ruby
 authors: 
 - Semin Lee
@@ -30,7 +30,7 @@ cert_chain:
   35w+y1Jd
   -----END CERTIFICATE-----
 
-date: 2008-12-09 00:00:00 +00:00
+date: 2008-12-15 00:00:00 +00:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -81,7 +81,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 1.1.0
+        version: 1.2.1
     version: 
 - !ruby/object:Gem::Dependency 
   name: hoe