qu-seqcluster 1.0.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: e998132776509d1b787ab5ba02ebf81c43179ce9
+  data.tar.gz: ec82c798b27f9eaeb12f8554be750adb46b1a8d7
+SHA512:
+  metadata.gz: f8027e2bfa6f14d3d9c7664f2efac98de8dc19e8786552c47ce759c2cf4a7912b8cf5b77b86112ea3b44e7ae98e01fd66be86363ee768ed22adf2f6c88ad8ccf
+  data.tar.gz: 51ad5ab6631c161db2e08025c6228fed584dfb640cde2cc1a956dc23e3373689708f0476b4620e8664fb3f3062a551b4ec13a84728f0ae5692d3749054ea0693

data/.gitignore

@@ -0,0 +1,19 @@
+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+test
+.DS_store

data/Gemfile

@@ -0,0 +1,5 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in qu-seqcluster.gemspec
+gemspec
+gem 'qu-utils'

data/LICENSE.txt

@@ -0,0 +1,22 @@
+Copyright (c) 2013 Wubin Qu
+
+MIT License
+
+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 +1,45 @@
+# Qu::Seqcluster
+
+Cluster DNA/RNA based on k-mer algorithm
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'qu-seqcluster'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install qu-seqcluster
+
+## Usage
+
+```
+Usage: seqcluster -i seq.fasta -k 9 -c 0.9
+
+Required options:
+
+    -i, --in File                    Input sequence file in fasta format.
+
+Optional options:
+
+    -k, --kvalue Integer             K value, default is 9.
+    -o, --out File                   Output file name for storing the results, default is screen.
+    -c, --cutoff Float               Cutoff value for the similarity for cluster, default is 0.9.
+
+
+    -h, --help                       Show this message and quit
+    -v, --version                    Show version
+```
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

@@ -0,0 +1 @@
+require "bundler/gem_tasks"

data/bin/seqcluster

@@ -0,0 +1,6 @@
+#!/usr/bin/env ruby
+
+require 'qu/seqcluster'
+
+opts = Qu::Seqcluster::Options.new(ARGV).opts
+Qu::Seqcluster::Runner.new(opts).run

data/lib/qu/seqcluster.rb

@@ -0,0 +1,13 @@
+require "qu/utils"
+
+require_relative "seqcluster/program"
+require_relative "seqcluster/version"
+require_relative "seqcluster/options"
+require_relative "seqcluster/cluster"
+require_relative "seqcluster/runner"
+
+module Qu
+  module Seqcluster
+    # Your code goes here...
+  end
+end

data/lib/qu/seqcluster/cluster.rb

@@ -0,0 +1,53 @@
+require 'set'
+
+module Qu
+  module Seqcluster
+    class Cluster
+      attr_reader :opts
+      def initialize(opts)
+        @opts = opts
+      end
+
+      def find_cluster
+        records = Bio::FlatFile.new(Bio::FastaFormat, File.open(@opts.in)).to_a
+        records.sort_by! {|r| -r.seq.size}
+
+        groups = []
+        while records.size > 0
+          groups << []
+          seed_record = records.shift
+          groups[-1] << seed_record
+          seed_kmer_set = seed_kmer(seed_record, @opts.kvalue, 1)
+          records.each_entry do |record|
+            plus = cal_similarity(record.naseq, @opts.kvalue, seed_kmer_set)
+            minus = cal_similarity(record.naseq.reverse_complement, @opts.kvalue, seed_kmer_set)
+
+            similarity, strand = plus > minus ? [plus, '+'] : [minus, '-']
+
+            if similarity >= @opts.cutoff
+              groups[-1] << [record, similarity, strand]
+            end
+          end
+          records.delete_if {|record| groups[-1].collect {|group_record, similarity, strand| group_record}.include?(record)}
+        end
+
+        return groups
+      end
+
+      private
+
+      def seed_kmer(record, window, step)
+        mer_set = Set.new
+        record.naseq.window_search(window, step) {|s| mer_set.add(s.to_sym)}
+        return mer_set
+      end
+
+      def cal_similarity(seq, k, seed_kmer_set)
+        sum = 0
+        remainder = seq.window_search(k, k) {|s| sum += 1 if seed_kmer_set.include?(s.to_sym)}
+        return (sum.to_f * k) / (seq.size - remainder.size)
+      end
+
+    end # Cluster
+  end
+end

data/lib/qu/seqcluster/options.rb

@@ -0,0 +1,106 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'ostruct'
+
+module Qu
+  module Seqcluster
+
+    module_function
+
+    def default_options
+      options = OpenStruct.new
+      options.in = nil
+      options.out = $stdout
+
+      options.kvalue = 9
+      options.cutoff = 0.9
+
+      return options
+    end
+
+    class Options
+
+      attr_reader :opts
+
+      def initialize(argv)
+        @opts = parse_opts(argv)
+      end
+
+
+      def parse_opts(argv)
+
+        options = Seqcluster::default_options
+
+        OptionParser.new do |opts|
+          opts.banner = "#{PROGRAM} [#{VERSION}]: Cluster DNA/RNA based on k-mer algorithm
+Usage: #{PROGRAM} -i seq.fasta -k 9 -c 0.9"
+
+          opts.separator ""
+          opts.separator "Required options:"
+          opts.separator ""
+
+          opts.on('-i', '--in File', String, 'Input sequence file in fasta format.') do |value|
+            if File.directory?(value)
+              $stderr.puts "Error: #{value} is a direcotry."
+              exit
+            end
+
+            unless File.exists?(value)
+              $stderr.puts "Error: #{value} is not exists."
+              exit
+            end
+            options.in = value
+          end
+
+          opts.separator ""
+          opts.separator "Optional options:"
+          opts.separator ""
+
+          opts.on('-k', '--kvalue Integer', Integer, "K value, default is #{options.kvalue}.") do |value|
+            options.kvalue = value
+          end
+
+          opts.on("-o", "--out File", String, "Output file name for storing the results, default is screen.") do |value|
+            options.out = File.open(value, 'w')
+          end
+
+          opts.on('-c', '--cutoff Float', Float, "Cutoff value for the similarity for cluster, default is #{options.cutoff}.") do |value|
+            options.cutoff = value
+          end
+
+          opts.separator ""
+          opts.separator ""
+
+          opts.on("-h", "--help", "Show this message and quit") do
+            puts opts
+            exit
+          end
+
+          opts.on("-v", "--version", "Show version") do
+            puts "#{PROGRAM} #{VERSION}"
+            exit
+          end
+
+          opts.separator ""
+          opts.separator "Author: Wubin Qu <quwubin@gmail.com>"
+          opts.separator ""
+
+          begin
+            argv = ["-h"] if argv.empty?
+            opts.parse!(argv)
+          rescue OptionParser::ParseError => e
+            $stderr.puts e.message, "\n", opts
+            exit
+          end
+
+          if options.in.nil?
+            $stderr.puts "Error: option -i required."
+            exit
+          end
+        end
+        return options
+      end
+    end
+  end
+end

data/lib/qu/seqcluster/program.rb

@@ -0,0 +1,5 @@
+module Qu
+  module Seqcluster
+    PROGRAM = 'seqcluster'
+  end
+end

data/lib/qu/seqcluster/runner.rb

@@ -0,0 +1,29 @@
+require_relative 'options'
+require_relative 'cluster'
+
+module Qu
+  module Seqcluster
+    class Runner
+      attr_reader :opts
+      def initialize(opts)
+        @opts = opts
+      end
+
+      def run
+        groups = Cluster.new(@opts).find_cluster
+        output(groups)
+      end
+
+      def output(groups)
+        @opts.out.puts "Cluster count: #{groups.size}"
+        groups.each_with_index do |group, group_index|
+          @opts.out.puts "Cluster #{group_index + 1}: #{group[0].entry_id}"
+          group[1..-1].each do |record, similarity, strand|
+            @opts.out.puts "\tMember: #{record.entry_id} [#{strand}/#{similarity.round(2)}]"
+          end
+        end
+      end
+
+    end
+  end
+end

data/lib/qu/seqcluster/version.rb

@@ -0,0 +1,5 @@
+module Qu
+  module Seqcluster
+    VERSION = "1.0.0"
+  end
+end

data/qu-seqcluster.gemspec

@@ -0,0 +1,25 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'qu/seqcluster/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "qu-seqcluster"
+  spec.version       = Qu::Seqcluster::VERSION
+  spec.authors       = ["Wubin Qu"]
+  spec.email         = ["quwubin@gmail.com"]
+  spec.description   = %q{Cluster DNA/RNA based on k-mer algorithm}
+  spec.summary       = %q{k-mer based cluster program}
+  spec.homepage      = "https://github.com/quwubin/qu-seqcluster"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_runtime_dependency 'qu-utils', '~> 1.0'
+
+  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "rake"
+end

metadata

@@ -0,0 +1,100 @@
+--- !ruby/object:Gem::Specification
+name: qu-seqcluster
+version: !ruby/object:Gem::Version
+  version: 1.0.0
+platform: ruby
+authors:
+- Wubin Qu
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-04-28 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: qu-utils
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rake
+  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'
+description: Cluster DNA/RNA based on k-mer algorithm
+email:
+- quwubin@gmail.com
+executables:
+- seqcluster
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/seqcluster
+- lib/qu/seqcluster.rb
+- lib/qu/seqcluster/cluster.rb
+- lib/qu/seqcluster/options.rb
+- lib/qu/seqcluster/program.rb
+- lib/qu/seqcluster/runner.rb
+- lib/qu/seqcluster/version.rb
+- qu-seqcluster.gemspec
+homepage: https://github.com/quwubin/qu-seqcluster
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.0
+signing_key: 
+specification_version: 4
+summary: k-mer based cluster program
+test_files: []