ulla 0.9.7 → 0.9.8

data/History.txt

@@ -1,3 +1,7 @@
+== 0.9.8 21/07/2009
+
+* Fixed a bug in generating amino acids symbols when --cys 2 is set
+
 == 0.9.7 30/05/2009
 
 * Added --environment option to consider not only substituted amino acids' environments but also substituting amino acids' environments

data/Manifest.txt

@@ -1,4 +1,3 @@
-.autotest
 History.txt
 Manifest.txt
 PostInstall.txt

data/README.rdoc

@@ -49,7 +49,10 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
     --classdef (-c) FILE: a file for the defintion of environments (default: 'classdef.dat')
     --outfile (-o) FILE: output filename (default 'allmat.dat')
     --weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (default: 60)
-    --noweight: calculate substitution count with no weights
+    --noweight: calculate substitution counts with no weights
+    --environment (-e) INTEGER:
+        0 for considering only substituted amino acids' environments (default)
+        1 for considering both substituted and substituting amino acids' environments
     --smooth (-s) INTEGER:
         0 for partial smoothing (default)
         1 for full smoothing
@@ -60,14 +63,14 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
         1 for both structure and sequence
         2 for using only C for both (must be set when you have no 'disulphide' or 'disulfide' annotation in templates)
     --output INTEGER:
-        0 for raw count (no smoothing performed)
+        0 for raw counts (no smoothing performed)
         1 for probabilities
-        2 for log odds ratios (default)
+        2 for log-odds (default)
     --noroundoff: do not round off log odds ratio
-    --scale INTEGER: log odds ratio matrices in 1/n bit units (default 3)
+    --scale INTEGER: log-odds matrices in 1/n bit units (default 3)
     --sigma DOUBLE: change the sigma value for smoothing (default 5.0)
     --autosigma: automatically adjust the sigma value for smoothing
-    --add DOUBLE: add this value to raw count when deriving log odds ratios without smoothing (default 1/#classes)
+    --add DOUBLE: add this value to raw counts when deriving log-odds without smoothing (default 0)
     --pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
     --pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
     --heatmap INTEGER:
@@ -234,8 +237,6 @@ It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~ken
 
 == TODO
 
-* Substitution table generation considering both the source and the target environmental classes
-
 == Repository
 
 You can download a pre-built RubyGems package from

data/Rakefile

@@ -1,32 +1,25 @@
-%w[rubygems rake rake/clean fileutils newgem rubigen].each { |f| require f }
-require File.dirname(__FILE__) + '/lib/ulla'
+require 'rubygems'
+gem 'hoe', '>= 2.1.0'
+require 'hoe'
+require 'fileutils'
+
+Hoe.plugin :newgem
+# Hoe.plugin :website
+# Hoe.plugin :cucumberfeatures
 
 # Generate all the Rake tasks
 # Run 'rake -T' to see list of generated tasks (from gem root directory)
-$hoe = Hoe.new('ulla', Ulla::VERSION) do |p|
-  p.developer('Semin Lee', 'seminlee@gmail.com')
-  p.changes               = p.paragraphs_of("History.txt", 0..1).join("\n\n")
-  p.post_install_message  = 'PostInstall.txt' # TODO remove if post-install message not required
-  p.rubyforge_name        = p.name # TODO this is default value
-  p.extra_deps            = [
+$hoe = Hoe.spec 'ulla' do
+  self.developer 'Semin Lee', 'seminlee@gmail.com'
+  self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
+  self.rubyforge_name       = self.name # TODO this is default value
+  self.extra_deps           = [
     ['narray',  '>= 0.5.9.5'],
     ['bio',     '>= 1.2.1'],
     ['facets',  '>= 2.4.5'],
     ['rmagick', '>= 2.9.1'],
   ]
-
-  p.extra_dev_deps = [
-    ['newgem', ">= #{::Newgem::VERSION}"]
-  ]
-
-  p.clean_globs |= %w[**/.DS_Store tmp *.log *.swp]
-  path = (p.rubyforge_name == p.name) ? p.rubyforge_name : "\#{p.rubyforge_name}/\#{p.name}"
-  p.remote_rdoc_dir = File.join(path.gsub(/^#{p.rubyforge_name}\/?/,''), 'rdoc')
-  p.rsync_args = '-av --delete --ignore-errors'
 end
 
-require 'newgem/tasks' # load /tasks/*.rake
+require 'newgem/tasks'
 Dir['tasks/**/*.rake'].each { |t| load t }
-
-# TODO - want other tests/tasks run by default? Add them to the list
-# task :default => [:spec, :features]

data/lib/ulla.rb

@@ -2,5 +2,5 @@ $:.unshift(File.dirname(__FILE__)) unless
   $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
 
 module Ulla
-  VERSION = '0.9.7'
+  VERSION = '0.9.8'
 end

data/lib/ulla/cli.rb

@@ -384,7 +384,7 @@ Options:
 
         # if --cys option 2, then we don't care about 'J' (for both Cystine and Cystine)
         if $cys == 2
-          $amino_acids = 'ACDEFGHIKLMNPQRSTVWY'.delete('J')
+          $amino_acids = 'ACDEFGHIKLMNPQRSTVWY'.delete('J').split('')
         end
 
         # create an EnvironmentFeatureArray object for storing all environment
@@ -709,11 +709,11 @@ Options:
                     env_label2  = $environment == 1 ? aa2 + '-' + aa1[1..-1] : env_labels[id2][pos]
 
                     if $cst_features.empty?
-                      $env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt)
-                      $env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt)
+                      $env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt) #rescue $logger.error "Something wrong with #{tem_file}-#{id2}-#{pos}-#{aa2}-#{env_label2}"
+                      $env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt) #rescue $logger.error "Something wrong with #{tem_file}-#{id2}-#{pos}-#{aa2}-#{env_label2}"
                     elsif (env_labels[id1][pos].split('').values_at(*$cst_features) == env_labels[id2][pos].split('').values_at(*$cst_features))
                       $env_classes[env_label1].increase_residue_count(aa2[0].chr, jnt_cnt)
-                      $env_classes[env_label2].increase_residue_count(aa1[1].chr, jnt_cnt)
+                      $env_classes[env_label2].increase_residue_count(aa1[0].chr, jnt_cnt)
                     else
                       $logger.debug "Skipped #{id1}-#{pos}-#{aa1[0].chr} and #{id2}-#{pos}-#{aa2[0].chr} having different symbols for constrained environment features each other."
                       next

data/ulla.gemspec

@@ -2,44 +2,43 @@
 
 Gem::Specification.new do |s|
   s.name = %q{ulla}
-  s.version = "0.9.6"
+  s.version = "0.9.7"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Semin Lee"]
-  s.date = %q{2009-04-16}
+  s.date = %q{2009-06-11}
   s.default_executable = %q{ulla}
   s.description = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
   s.email = ["seminlee@gmail.com"]
   s.executables = ["ulla"]
   s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "website/index.txt"]
-  s.files = [".autotest", "History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/ulla", "config/website.yml", "config/website.yml.sample", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "lib/ulla.rb", "lib/ulla/cli.rb", "lib/ulla/environment.rb", "lib/ulla/environment_class_hash.rb", "lib/ulla/environment_feature.rb", "lib/ulla/environment_feature_array.rb", "lib/ulla/heatmap_array.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/test_ulla.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "ulla.gemspec", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
-  s.has_rdoc = true
+  s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/ulla", "config/website.yml", "config/website.yml.sample", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "lib/ulla.rb", "lib/ulla/cli.rb", "lib/ulla/environment.rb", "lib/ulla/environment_class_hash.rb", "lib/ulla/environment_feature.rb", "lib/ulla/environment_feature_array.rb", "lib/ulla/heatmap_array.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/test_ulla.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "ulla.gemspec", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
   s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/ulla}
   s.post_install_message = %q{PostInstall.txt}
   s.rdoc_options = ["--main", "README.rdoc"]
   s.require_paths = ["lib"]
   s.rubyforge_project = %q{ulla}
-  s.rubygems_version = %q{1.3.1}
+  s.rubygems_version = %q{1.3.4}
   s.summary = %q{'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
-  s.test_files = ["test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb", "test/test_helper.rb", "test/test_ulla.rb"]
+  s.test_files = ["test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "test/test_ulla.rb", "test/ulla/test_cli.rb", "test/ulla/test_environment_class_hash.rb", "test/ulla/test_environment_feature.rb"]
 
   if s.respond_to? :specification_version then
     current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
-    s.specification_version = 2
+    s.specification_version = 3
 
     if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<narray>, [">= 0.5.9.5"])
       s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
       s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
       s.add_runtime_dependency(%q<rmagick>, [">= 2.9.1"])
-      s.add_development_dependency(%q<newgem>, [">= 1.3.0"])
+      s.add_development_dependency(%q<newgem>, [">= 1.4.1"])
       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<rmagick>, [">= 2.9.1"])
-      s.add_dependency(%q<newgem>, [">= 1.3.0"])
+      s.add_dependency(%q<newgem>, [">= 1.4.1"])
       s.add_dependency(%q<hoe>, [">= 1.8.0"])
     end
   else
@@ -47,7 +46,7 @@ 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<rmagick>, [">= 2.9.1"])
-    s.add_dependency(%q<newgem>, [">= 1.3.0"])
+    s.add_dependency(%q<newgem>, [">= 1.4.1"])
     s.add_dependency(%q<hoe>, [">= 1.8.0"])
   end
 end

data/website/index.html

@@ -4,7 +4,7 @@
 <head>
   <meta http-equiv="Refresh" content="5; URL=http://github.com/semin/ulla">
   <title>
-      ulla: a program for calculating environment-specific substitution tables
+      Ulla: a program for calculating environment-specific substitution tables
   </title>
 </head>
 <body>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: ulla
 version: !ruby/object:Gem::Version 
-  version: 0.9.7
+  version: 0.9.8
 platform: ruby
 authors: 
 - Semin Lee
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-05-30 00:00:00 +01:00
+date: 2009-07-21 00:00:00 +01:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -52,16 +52,6 @@ dependencies:
       - !ruby/object:Gem::Version 
         version: 2.9.1
     version: 
-- !ruby/object:Gem::Dependency 
-  name: newgem
-  type: :development
-  version_requirement: 
-  version_requirements: !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        version: 1.4.1
-    version: 
 - !ruby/object:Gem::Dependency 
   name: hoe
   type: :development
@@ -70,7 +60,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 1.8.0
+        version: 2.3.2
     version: 
 description: "'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes."
 email: 
@@ -83,10 +73,8 @@ extra_rdoc_files:
 - History.txt
 - Manifest.txt
 - PostInstall.txt
-- README.rdoc
 - website/index.txt
 files: 
-- .autotest
 - History.txt
 - Manifest.txt
 - PostInstall.txt
@@ -150,7 +138,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: ulla
-rubygems_version: 1.3.3
+rubygems_version: 1.3.4
 signing_key: 
 specification_version: 3
 summary: "'ulla' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes."

data/.autotest

@@ -1,5 +0,0 @@
-#require 'autotest/screen'
-
-#Autotest::Screen.statusline = '%H %`%-w%{=b bw}%n %t%{-}%+w (your statusline)'
-#Autotest::Screen.statusline = '%{=b}%{G} Screen(s): %{b}%w %=%{kG}%C%A  %D, %M/%d/%Y (your statusline)'
-