bio-locus 0.0.6 → 0.0.7

checksums.yaml

@@ -1,7 +1,7 @@
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data/.travis.yml

@@ -1,8 +1,6 @@
 language: ruby
 rvm:
-  - 1.9.2
-  - 1.9.3
-  - jruby-19mode # JRuby in 1.9 mode
+  - 2.2.2
 
 # - rbx-19mode
 #  - 1.8.7

data/Gemfile

@@ -1,14 +1,5 @@
 source "http://rubygems.org"
 group :development do
-  gem "cucumber"
-  gem "jeweler" 
-  gem "bundler"
+  gem "rake"
   gem "rspec"
-  gem "tokyocabinet"
-  gem "localmemcache"
-  gem "moneta"
 end
-# The following are optional (Ruby serialize is the default)
-# gem "tokyocabinet"
-# gem "localmemcache"
-# gem "moneta"

data/README.md

@@ -1,6 +1,6 @@
 # bio-locus
 
-[![Build Status](https://secure.travis-ci.org/pjotrp/bioruby-locus.png)](http://travis-ci.org/pjotrp/bioruby-locus)
+[![Build Status](https://secure.travis-ci.org/pjotrp/bio-locus.png)](http://travis-ci.org/pjotrp/bio-locus)
 
 Bio-locus is a tool for fast querying of genome locations. Many file
 formats in bioinformatics contain records that start with a chromosome
@@ -16,6 +16,15 @@ Why would you use bio-locus?
 3. See what positions match an EVS or GoNL database
 4. Compare locations from databases such as the TCGA and COSMIC
 5. Comparison of overlap or difference
+6. Parse and store values to reuse later (nyi)
+7. Store seek positions (nyi)
+
+How does bio-locus differ from tabix? Tabix is a fast indexer for
+tabular data. bio-locus does something similar. The difference is that
+bio-locus is more flexible in matching location data, is line 
+based with regex options, can use other back-ends (RAM,
+NoSQL, SQL), and does *not* use bgzip. In other words, bio-locus
+is friendly and more flexible.
 
 In principle any of the Moneta supported backends can be used,
 including LocalMemCache, RubySerialize and TokyoCabinet. The default
@@ -203,7 +212,7 @@ So now we have 99 INDELs for this dataset which are not common INDELs.
 Information on the source tree, documentation, examples, issues and
 how to contribute, see
 
-  http://github.com/pjotrp/bioruby-locus
+  http://github.com/pjotrp/bio-locus
 
 The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
 

data/Rakefile

@@ -1,30 +1,8 @@
 # encoding: utf-8
 
 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'
-Jeweler::Tasks.new do |gem|
-  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
-  gem.name = "bio-locus"
-  gem.homepage = "http://github.com/pjotrp/bioruby-locus"
-  gem.license = "MIT"
-  gem.summary = %Q{Fast storage and comparison of chr+pos(+alt) locations}
-  gem.description = %Q{A tool for fast querying and filtering of genome locations in VCF and other formats}
-  gem.email = "pjotr.public01@thebird.nl"
-  gem.authors = ["Pjotr Prins"]
-  # dependencies defined in Gemfile
-end
-Jeweler::RubygemsDotOrgTasks.new
-
 require 'rspec/core'
 require 'rspec/core/rake_task'
 RSpec::Core::RakeTask.new(:spec) do |spec|

data/VERSION

@@ -1 +1 @@
-0.0.6
+0.0.7

data/spec/bio-locus_spec.rb

@@ -12,26 +12,28 @@ describe "BioLocus with Serialize" do
   File.unlink(fn)
 end
 
-describe "BioLocus with Moneta" do
-  fn = 'biolocus_moneta_localmemcache.db'
-  store = BioLocus::MonetaMapper.new(:LocalMemCache,fn)
-  store['test'] = 'yes'
-  store['test2'] = 'no'
-  a = store['test']
-  store['test'].should == 'yes'
-  store['test2'].should  == 'no'
-  store.close
-  File.unlink(fn)
-end
+if false
+  describe "BioLocus with Moneta" do
+    fn = 'biolocus_moneta_localmemcache.db'
+    store = BioLocus::MonetaMapper.new(:LocalMemCache,fn)
+    store['test'] = 'yes'
+    store['test2'] = 'no'
+    a = store['test']
+    store['test'].should == 'yes'
+    store['test2'].should  == 'no'
+    store.close
+    File.unlink(fn)
+  end
 
-describe "BioLocus with TokyoCabinet" do
-  fn = 'biolocus_tokyocabinet.db'
-  store = BioLocus::TokyoCabinetMapper.new(fn)
-  store['test'] = 'yes'
-  store['test2'] = 'no'
-  a = store['test']
-  store['test'].should == 'yes'
-  store['test2'].should  == 'no'
-  store.close
-  File.unlink(fn)
+  describe "BioLocus with TokyoCabinet" do
+    fn = 'biolocus_tokyocabinet.db'
+    store = BioLocus::TokyoCabinetMapper.new(fn)
+    store['test'] = 'yes'
+    store['test2'] = 'no'
+    a = store['test']
+    store['test'].should == 'yes'
+    store['test2'].should  == 'no'
+    store.close
+    File.unlink(fn)
+  end
 end

metadata

@@ -1,113 +1,15 @@
 --- !ruby/object:Gem::Specification
 name: bio-locus
 version: !ruby/object:Gem::Version
-  version: 0.0.6
+  version: 0.0.7
 platform: ruby
 authors:
 - Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-10 00:00:00.000000000 Z
-dependencies:
-- !ruby/object:Gem::Dependency
-  name: cucumber
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: rspec
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: tokyocabinet
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: localmemcache
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: moneta
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
+date: 2015-09-14 00:00:00.000000000 Z
+dependencies: []
 description: A tool for fast querying and filtering of genome locations in VCF and
   other formats
 email: pjotr.public01@thebird.nl
@@ -127,9 +29,6 @@ files:
 - Rakefile
 - VERSION
 - bin/bio-locus
-- features/bio-locus.feature
-- features/step_definitions/bio-locus_steps.rb
-- features/support/env.rb
 - lib/bio-locus.rb
 - lib/bio-locus/dbmapper.rb
 - lib/bio-locus/locus.rb
@@ -141,7 +40,7 @@ files:
 - test/data/input/multisample.vcf
 - test/data/input/somaticsniper.vcf
 - test/data/input/test.snv1
-homepage: http://github.com/pjotrp/bioruby-locus
+homepage: http://github.com/pjotrp/bio-locus
 licenses:
 - MIT
 metadata: {}
@@ -161,7 +60,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.3
+rubygems_version: 2.4.5.1
 signing_key: 
 specification_version: 4
 summary: Fast storage and comparison of chr+pos(+alt) locations

data/features/bio-locus.feature

@@ -1,9 +0,0 @@
-Feature: something something
-  In order to something something
-  A user something something
-  something something something
-
-  Scenario: something something
-    Given inspiration
-    When I create a sweet new gem
-    Then everyone should see how awesome I am

data/features/support/env.rb

@@ -1,13 +0,0 @@
-require 'bundler'
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
-
-$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
-require 'bio-locus'
-
-require 'rspec/expectations'