ms-core 0.0.17 → 0.0.18

data/Rakefile

@@ -1,12 +1,4 @@
 require 'rubygems'
-require 'bundler'
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
 require 'rake'
 
 require 'jeweler'
@@ -16,11 +8,13 @@ Jeweler::Tasks.new do |gem|
   gem.homepage = "http://github.com/jtprince/ms-core"
   gem.license = "MIT"
   gem.summary = %Q{basic, shared functionality for mspire libraries}
-  gem.description = %Q{basic, shared functionality for mspire libraries}
+  gem.description = %Q{basic, shared functionality for mspire libraries.}
   gem.email = "jtprince@gmail.com"
   gem.authors = ["John T. Prince", "Simon Chiang"]
   gem.rubyforge_project = 'mspire'
-  # Dependencies in Gemfile
+  gem.add_runtime_dependency 'bio', '>= 1.4.1'
+  gem.add_development_dependency "spec-more", ">= 0"
+  gem.add_development_dependency "jeweler", "~> 1.5.2"
 end
 Jeweler::RubygemsDotOrgTasks.new
 
@@ -31,12 +25,12 @@ Rake::TestTask.new(:spec) do |spec|
   spec.verbose = true
 end
 
-require 'rcov/rcovtask'
-Rcov::RcovTask.new do |spec|
-  spec.libs << 'spec'
-  spec.pattern = 'spec/**/*_spec.rb'
-  spec.verbose = true
-end
+#require 'rcov/rcovtask'
+#Rcov::RcovTask.new do |spec|
+#  spec.libs << 'spec'
+#  spec.pattern = 'spec/**/*_spec.rb'
+#  spec.verbose = true
+#end
 
 task :default => :spec
 

data/VERSION

@@ -1 +1 @@
-0.0.17
+0.0.18

data/lib/ms/fasta.rb

@@ -55,5 +55,31 @@ module Ms
       Bio::FlatFile.new(Bio::FastaFormat, io)
     end
 
+    # returns two hashes [id_to_length, id_to_description]
+    # faster (~4x) than official route.
+    def self.protein_lengths_and_descriptions(file)
+      protid_to_description = {}
+      protid_to_length = {}
+      re = /^>([^\s]+) (.*)/
+        ids = []
+      lengths = []
+      current_length = nil
+      IO.foreach(file) do |line|
+        line.chomp!
+        if md=re.match(line)  
+          lengths << current_length
+          current_id = md[1]
+          ids << current_id
+          current_length = 0
+          protid_to_description[current_id] = md[2]
+        else
+          current_length += line.size
+        end
+      end
+      lengths << current_length
+      lengths.shift # remove the first nil entry
+      [Hash[ids.zip(lengths).to_a], protid_to_description]
+    end
+
   end
 end

data/spec/ms/fasta_spec.rb

@@ -41,6 +41,10 @@ describe 'basic fasta operations' do
     end
   end
 
+  xit 'can deliver length and description hashes' do
+    # need to test
+  end
+
   it 'can read a file' do
     %w(newlines_file carriage_returns_and_newlines_file).each do |file|
       Ms::Fasta.open(@data[file]) do |fasta|

data/spec/spec_helper.rb

@@ -1,13 +1,4 @@
 require 'rubygems'
-require 'bundler'
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
-require 'benchmark'
 require 'spec/more'
 
 $LOAD_PATH.unshift(File.dirname(__FILE__))

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 17
-  version: 0.0.17
+  - 18
+  version: 0.0.18
 platform: ruby
 authors: 
 - John T. Prince
@@ -15,11 +15,12 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-09 00:00:00 -07:00
+date: 2011-03-31 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: bio
+  prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -31,10 +32,10 @@ dependencies:
         - 1
         version: 1.4.1
   type: :runtime
-  prerelease: false
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
   name: spec-more
+  prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -44,26 +45,11 @@ dependencies:
         - 0
         version: "0"
   type: :development
-  prerelease: false
   version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: bundler
-  requirement: &id003 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 0
-        - 0
-        version: 1.0.0
-  type: :development
-  prerelease: false
-  version_requirements: *id003
 - !ruby/object:Gem::Dependency 
   name: jeweler
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ~>
@@ -74,22 +60,8 @@ dependencies:
         - 2
         version: 1.5.2
   type: :development
-  prerelease: false
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: rcov
-  requirement: &id005 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        version: "0"
-  type: :development
-  prerelease: false
-  version_requirements: *id005
-description: basic, shared functionality for mspire libraries
+  version_requirements: *id003
+description: basic, shared functionality for mspire libraries.
 email: jtprince@gmail.com
 executables: []
 
@@ -98,8 +70,6 @@ extensions: []
 extra_rdoc_files: 
 - README.rdoc
 files: 
-- Gemfile
-- Gemfile.lock
 - History
 - MIT-LICENSE
 - README.rdoc
@@ -144,7 +114,6 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 268691801649348521
       segments: 
       - 0
       version: "0"

data/Gemfile

@@ -1,14 +0,0 @@
-source "http://rubygems.org"
-# Add dependencies required to use your gem here.
-# Example:
-#   gem "activesupport", ">= 2.3.5"
-gem 'bio', '>= 1.4.1'
-
-# Add dependencies to develop your gem here.
-# Include everything needed to run rake, tests, features, etc.
-group :development do
-  gem "spec-more", ">= 0"
-  gem "bundler", "~> 1.0.0"
-  gem "jeweler", "~> 1.5.2"
-  gem "rcov", ">= 0"
-end

data/Gemfile.lock

@@ -1,24 +0,0 @@
-GEM
-  remote: http://rubygems.org/
-  specs:
-    bacon (1.1.0)
-    bio (1.4.1)
-    git (1.2.5)
-    jeweler (1.5.2)
-      bundler (~> 1.0.0)
-      git (>= 1.2.5)
-      rake
-    rake (0.8.7)
-    rcov (0.9.9)
-    spec-more (0.0.4)
-      bacon
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  bio (>= 1.4.1)
-  bundler (~> 1.0.0)
-  jeweler (~> 1.5.2)
-  rcov
-  spec-more