bio-locus 0.0.2

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 33548bcc8a3474a7e1d3ebbec6c4cfe2472d4af9
+  data.tar.gz: e7c7f93a5638a79f2052142d472dbad3dc57b334
+SHA512:
+  metadata.gz: 04b8576748a2f324c7e4de0224c1b7409e28da8e2e2697e5bf0da60a55db0a8994a6185649d4c3b68930e7d617732e92edd8aed54cba4646cea14ded86f09be6
+  data.tar.gz: 2b17b04ef00b04a37a1d272ee4a10137fc50392a108850671f13d01a777755674413c6bf21e26843a700168d57484cb0fd150c0a054adf012d4c2577f973e6a8

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

@@ -0,0 +1 @@
+--color

data/.travis.yml

@@ -0,0 +1,13 @@
+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+
+# - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

@@ -0,0 +1,14 @@
+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "cucumber"
+  gem "jeweler" 
+  gem "bundler"
+end
+gem "localmemcache"
+gem "moneta"

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2014 Pjotr Prins
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -0,0 +1,162 @@
+# bio-locus
+
+[![Build Status](https://secure.travis-ci.org/pjotrp/bioruby-locus.png)](http://travis-ci.org/pjotrp/bioruby-locus)
+
+Bio-locus is a tool for fast querying of genome locations. Many file
+formats in bioinformatics contain records that start with a chromosome
+name and a position for a SNP, or a start-end position for indels.
+
+This tool essentially allows your to store this information in a Hash
+or database:
+
+```sh
+  bio-locus --store < one.vcf 
+```
+
+which creates or adds to a cache file or database with unique entries
+for all listed positions (chr+pos) AND for all listed positions with
+listed alt alleles. To find positions in another dataset which match
+those in the database:
+
+```sh
+  bio-locus --match < two.vcf
+```
+
+The point is that this is a two-step process, first create the
+indexed database, next query it. It is also possible to remove entries
+with the --delete switch.
+
+To match with alt use
+
+```sh
+  bio-locus --match --include-alt < two.vcf
+```
+
+Why would you use bio-locus?
+
+* To reduce the size of large SNP databases before storage/querying
+* To gain performance
+* To filter on chr+pos (default)
+* To filter on chr+pos+field (where field can be a VCF ALT)
+
+Use cases are 
+
+* To filter for annotated variants
+* To remove common variants from a set
+
+In short a more targeted approach allowing you to work with less data. This
+tool is decently fast. For example, looking for 130 positions in 20 million SNPs
+in GoNL takes 0.11s to store and 1.5 minutes to match on my laptop:
+
+```sh
+cat my_130_variants.vcf | ./bin/bio-locus --store
+  Stored 130 positions out of 130 in locus.db
+  real    0m0.119s
+  user    0m0.108s
+  sys     0m0.012s
+
+cat gonl.*.vcf |./bin/bio-locus --match
+  Matched 3 out of 20736323 lines in locus.db!
+  real    1m34.577s
+  user    1m33.602s
+  sys     0m1.868s
+```
+
+Note: for the storage the [moneta](https://github.com/minad/moneta) gem is used, currently with localmemcache.
+
+Note: the ALT field is split into components for matching, so A,C
+becomes two chr+pos records, one for A and one for C.
+
+## Installation
+
+```sh
+gem install bio-locus
+```
+
+## Command line
+
+In addition to --store and --match mentioned above there are a number
+of options available through
+
+```sh
+bio-locus --help
+```
+
+### Deleting keys
+
+To delete entries use 
+
+```sh
+  bio-locus --delete < two.vcf
+```
+
+To match with alt use
+
+```sh
+  bio-locus --delete --include-alt < two.vcf
+```
+
+You may need to run both with and without alt, depending on your needs!
+
+### Parsing
+
+It is possible to use any line based format. For example parsing the
+alt from
+
+```
+X       107976940       G/C     -1      5       5       0.75    H879D   0      IRS4     CCDS14544       Cat/Gat rs1801164       missense_variant        ENST00000372129.2:c.2635C>G
+```
+
+can be done with
+
+```sh
+bio-locus --store --eval-alt 'field[2].split(/\//)[1]'
+```
+
+### COSMIC
+
+COSMIC is pretty large, so it can be useful to cut the database down to the
+variants that you have. The locus information is combined
+in the before last column as chr:start-end, e.g.,
+19:58861911-58861911. This will work:
+
+```sh
+bio-locus -i --match --eval-chr='field[13] =~ /^([^:]+)/ ; $1' --eval-pos='field[13] =~ /:(\d+)-/ ; $1 ' < CosmicMutantExportIncFus_v68.tsv
+```
+
+Note the -i switch is needed to skip records that lack position
+information.
+
+## Usage
+
+```ruby
+require 'bio-locus'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/pjotrp/bioruby-locus
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-locus)
+
+## Copyright
+
+Copyright (c) 2014 Pjotr Prins. See LICENSE.txt for further details.
+

data/Rakefile

@@ -0,0 +1,52 @@
+# 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|
+#   spec.pattern = FileList['spec/**/*_spec.rb']
+# end
+
+# RSpec::Core::RakeTask.new(:rcov) do |spec|
+# spec.pattern = 'spec/**/*_spec.rb'
+# spec.rcov = true
+# end
+
+require 'cucumber/rake/task'
+Cucumber::Rake::Task.new(:features)
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-locus #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

@@ -0,0 +1 @@
+0.0.2

data/bin/bio-locus

@@ -0,0 +1,117 @@
+#!/usr/bin/env ruby
+#
+
+USAGE = "Use --help for info\n"
+
+gempath = File.dirname(File.dirname(__FILE__))
+$: << File.join(gempath,'lib')
+
+VERSION_FILENAME=File.join(gempath,'VERSION')
+version = File.new(VERSION_FILENAME).read.chomp
+
+if ARGV.size == 0
+  print USAGE
+end
+
+require 'bio-locus'
+require 'optparse'
+
+options = {task: nil, db: 'locus.db', show_help: false, header: 1}
+opts = OptionParser.new do |o|
+  o.banner = "Usage: #{File.basename($0)} [options] filename\ne.g. #{File.basename($0)} test.txt"
+
+  o.on("--store", 'Create or add to a cache file') do
+    options[:task] = :store
+    options[:include_alt] = true  # always include alt
+  end
+
+  o.on("--delete", 'Remove matches from a cache file') do
+    options[:task] = :delete
+  end
+
+  o.on("--match", 'Match a cache file') do
+    options[:task] = :match
+  end
+
+  o.on("--include-alt", 'Include chr+pos+ALT VCF field to filter') do
+    options[:include_alt] = true
+  end
+
+  o.on("--exclude-alt", 'Override adding chr+pos+ALT field to store') do
+    options[:exclude_alt] = true
+  end
+
+
+  o.on("--db filename",String,"Use db file") do | fn |
+    options[:db] = fn
+  end
+
+  o.on("--eval-chr expr",String,"Evaluate record to retrieve chr name") do | expr |
+    options[:eval_chr] = expr
+  end
+
+  o.on("--eval-pos expr",String,"Evaluate record to retrieve position") do | expr |
+    options[:eval_pos] = expr
+  end
+
+  o.on("--eval-alt expr",String,"Evaluate record to retrieve alt list") do | expr |
+    options[:eval_alt] = expr
+  end
+  
+  o.on("--header num", "Header lines (default 1)") do |l|
+    options[:header] = l.to_i
+  end
+   
+  o.on("-q", "--quiet", "Run quietly") do |q|
+    options[:quiet] = true
+  end
+   
+  o.on("-v", "--verbose", "Run verbosely") do |v|
+    options[:verbose] = true
+  end
+   
+  o.on("-d", "--debug", "Debug mode") do |v|
+    options[:debug] = true
+  end
+
+  o.on("-i", "--ignore-errors", "Continue on error") do 
+    options[:ignore_errors] = true
+  end
+
+
+  o.separator ""
+  o.on_tail('-h', '--help', 'display this help and exit') do
+    options[:show_help] = true
+  end
+end
+
+begin
+  opts.parse!(ARGV)
+
+ $stderr.print "bio-locus #{version} (biogem Ruby #{RUBY_VERSION}) by Pjotr Prins 2014\n" if !options[:quiet]
+
+  if options[:show_help] 
+    print opts 
+    print USAGE
+    exit 1
+  end
+
+  $stderr.print "Options: ",options,"\n" if !options[:quiet]
+
+rescue OptionParser::InvalidOption => e
+  options[:invalid_argument] = e.message
+end
+
+(0..options[:header]).each { STDIN.gets }
+
+case options[:task] 
+  when :store then
+    require 'bio-locus/store'
+    options[:include_alt]=false if options[:exclude_alt]
+    BioLocus::Store.run(options)
+  when :match ,:delete then
+    require 'bio-locus/match'
+    BioLocus::Match.run(options)
+  else
+    raise "I do not know what to do!"
+end

data/features/bio-locus.feature

@@ -0,0 +1,9 @@
+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

@@ -0,0 +1,13 @@
+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'

data/lib/bio-locus.rb

@@ -0,0 +1,12 @@
+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-locus/locus.rb'
+