scbi_ace 0.0.6

data/History.txt

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+=== 0.0.6 2012-07-25
+
+Added documentation
+
+=== 0.0.5 2012-07-24
+
+Added AceParser
+
+=== 0.0.1 2010-10-06
+
+* Initial release

data/Manifest.txt

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+History.txt
+Manifest.txt
+PostInstall.txt
+README.rdoc
+Rakefile
+lib/scbi_ace.rb
+script/console
+script/destroy
+script/generate
+test/test_helper.rb
+test/test_scbi_ace.rb
+lib/scbi_ace/indexed_ace_file.rb
+lib/scbi_ace/ace_parser.rb
+lib/scbi_ace/contig.rb
+lib/scbi_ace/read.rb

data/PostInstall.txt

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+
+For more information on scbi_ace, see http://scbi_ace.rubyforge.org
+
+NOTE: Change this information in PostInstall.txt 
+You can also delete it if you don't want it.
+
+

data/README.rdoc

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+= scbi_ace
+
+* http://www.scbi.uma.es/downloads
+
+== DESCRIPTION:
+
+scbi_ace is a ruby gem to read and parse ACE files containing contigs. It automatically indexes the input ace file to improve random access to contigs.
+
+== FEATURES/PROBLEMS:
+
+* Indexes ace files to provide fast random access to individual contigs
+* Parses the text representation in ACE format to Contigs and Reads objects
+* Generates the text representation 
+
+== SYNOPSIS:
+
+To get the text that defines a contig by its name:
+
+  require 'scbi_ace'
+  
+  ace=IndexedAceFile.new(File.join(File.dirname(__FILE__),'test.ace'))
+
+  puts ace.read_contig('Contig1')
+  
+  ace.close
+
+
+To parse all contigs in an ACE file
+
+  require 'scbi_ace'
+  
+  ace=AceParser.new(filename)
+
+  ace.each_contig do |contig|
+    puts contig.name
+    puts contig.reads.count
+  end
+
+  ace.close
+
+To parse one contig in an ACE file
+
+  require 'scbi_ace'
+
+  ace=AceParser.new(filename)
+
+  contig=ace.read_contig('Contig1')
+  puts contig.name
+  puts contig.reads.count
+  
+  # to get next contig (nil if none available)
+  contig2 = ace.next_contig
+  puts contig2.name
+  puts contig2.reads.count
+
+  ace.close
+  
+  
+== REQUIREMENTS:
+
+None
+
+== INSTALL:
+
+* gem install scbi_ace
+
+== LICENSE:
+
+(The MIT License)
+
+Copyright (c) 2010 Noe Fernandez & Dario Guerrero
+
+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/Rakefile

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+require 'rubygems'
+gem 'hoe', '>= 2.1.0'
+require 'hoe'
+require 'fileutils'
+require './lib/scbi_ace'
+
+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.spec 'scbi_ace' do
+  self.developer 'Noe Fernandez & Dario Guerrero', 'noefp@uma.es , dariogf@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         = [['activesupport','>= 2.0.2']]
+
+end
+
+require 'newgem/tasks'
+Dir['tasks/**/*.rake'].each { |t| load t }
+
+# TODO - want other tests/tasks run by default? Add them to the list
+# remove_task :default
+# task :default => [:spec, :features]

data/lib/scbi_ace.rb

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+$:.unshift(File.dirname(__FILE__)) unless
+  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
+
+$: << File.join(File.dirname(__FILE__),File.basename(__FILE__,File.extname(__FILE__)))
+
+require 'indexed_ace_file'
+require 'ace_parser'
+
+module ScbiAce
+   VERSION = '0.0.6'
+end

data/lib/scbi_ace/ace_parser.rb

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+# Description: This class provided the methods to parse and write an ACE file and to add contigs to the Ace
+# ---- Author: Noe Fernandez Pozo
+# ------ Date: 31-May-2011
+
+require 'contig'
+require 'indexed_ace_file'
+
+class AceParser < IndexedAceFile
+
+  # attr_accessor :name,:contigs,:reads_count
+
+  def initialize(ace_file)
+    super(ace_file)
+
+    # @ace_file = File.open(ace_file)
+    # reads_count = @ace_file.readline.sub(/^AS\s+\d+\s+/,'')
+
+  end
+
+  def close
+    super
+    # @ace_file.close
+  end
+
+  def next_contig
+    
+    res=super()
+  
+    if !res.nil?
+      contig = parse_contig(res)
+    end
+  
+    return contig
+  end
+  
+  def read_contig(contig_name)
+    res=super(contig_name)
+    
+    if !res.nil?
+      contig = parse_contig(res)
+    end
+  
+    return contig
+  end
+
+  def write_ace(contigs)
+
+    ace_to_print = []
+    reads_count=0
+    contigs.map {|c| reads_count+=c.reads.count}
+
+    ace_to_print.push "AS #{contigs.count} #{reads_count}"
+
+    contigs.each do |contig|
+      #---------------------------------------------- CO
+      ace_to_print.push "CO #{contig.name} #{contig.length} #{contig.reads_num} #{contig.bs_num} #{contig.orientation}"
+      ace_to_print.push contig.fasta.scan(/.{1,60}/m)
+
+      #---------------------------------------------- BQ
+      ace_to_print.push "\nBQ"
+      seq_qual = contig.qual.split(" ")
+      count = 0
+      qv_line = ''
+      seq_qual.each do |qv|
+        count+=1
+        qv_line << "#{qv} "
+        if (count % 60 == 0)
+          ace_to_print.push qv_line
+          qv_line = ''
+        end
+      end
+
+      ace_to_print.push ""
+      #---------------------------------------------- AF
+      af_array = []
+      contig.reads.each_value do |read|
+        ace_to_print.push "AF #{read.name} #{read.orientation} #{read.start_in_consensus}"
+        af_array.push read.name
+      end
+
+      #---------------------------------------------- BS
+      bs_array = []
+      contig.reads.each_value do |read|
+        bs_array = bs_array + read.bs
+      end
+
+      bs_array.sort!{|a,b| a['padded_start_consensus'].to_i<=>b['padded_start_consensus'].to_i}
+      bs_array.each do |bs_hash|
+        ace_to_print.push "BS #{bs_hash['padded_start_consensus']} #{bs_hash['padded_end_consensus']} #{bs_hash['read_name']}"
+      end
+
+      #----------------------------------------------- RD
+      af_array.each do |name|
+        contig.reads[name]
+        ace_to_print.push "\nRD #{name} #{contig.reads[name].padded_bases_num} #{contig.reads[name].item_num} #{contig.reads[name].tag_num}"
+        ace_to_print.push contig.reads[name].fasta.scan(/.{1,60}/m)
+        ace_to_print.push "\nQA #{contig.reads[name].qual_clip_start} #{contig.reads[name].qual_clip_end} #{contig.reads[name].align_clip_start} #{contig.reads[name].align_clip_end}"
+        ace_to_print.push "DS"
+      end
+    end
+
+    return ace_to_print.join("\n")
+
+  end
+
+  # def add_contig(contig_name,contig_length,reads_num,bs_num,orientation)
+  #   contig= Contig.new(contig_name,contig_length,reads_num,bs_num,orientation)
+  #
+  #   # @contigs.push contig
+  #   return contig
+  #
+  # end
+
+  def parse_contig(contig_lines)
+    contig = nil
+    read = nil
+    save_fasta = false
+    save_read_fasta = false
+    save_qual = false
+    contig_fasta = ''
+    read_fasta = ''
+    contig_qual = ''
+    bs = {}
+
+    # my_ace = File.open(@ace_file)
+    #         @reads_count = my_ace.readline.sub(/^AS\s+\d+\s+/,'')
+
+    contig_lines.split("\n").each do |line|
+      # @ace_file.each do |line|
+      line.chomp!
+      #---------------------------------------------- contig fasta
+      if (save_fasta)
+        if !(line =~ /^./)
+          contig.add_fasta(contig_fasta)
+          save_fasta = false
+          contig_fasta = ''
+        end
+        contig_fasta << line
+      end
+      #---------------------------------------------- contig qual
+      if (save_qual)
+        if !(line =~ /^./)
+          contig.add_qual(contig_qual)
+          save_qual = false
+          contig_qual = ''
+        end
+        contig_qual << line
+      end
+      #---------------------------------------------- read fasta
+      if (save_read_fasta)
+        if !(line =~ /^./)
+          read.add_fasta(read_fasta)
+          save_read_fasta = false
+          read_fasta = ''
+        end
+        read_fasta << line
+      end
+
+      #---------------------------------------------- CO
+      if (line =~ /^CO\s+([^\s]+)\s+([^\s]+)\s+([^\s]+)\s+([^\s]+)\s+([^\s]+)/)
+        contig_name = $1
+        contig_length = $2
+        reads_num = $3
+        bs_num = $4
+        orientation = $5
+        save_fasta = true
+        # contig = add_contig(contig_name,contig_length,reads_num,bs_num,orientation)
+        contig= Contig.new(contig_name,contig_length,reads_num,bs_num,orientation)
+      end
+
+      #---------------------------------------------- BQ
+      if (line =~ /^BQ/)
+        save_qual = true
+      end
+
+      #---------------------------------------------- AF
+      if (line =~ /^AF\s+([^\s]+)\s+([A-Z])\s+([^\s]+)/)
+        read_name = $1
+        orientation = $2
+        start_consensus = $3
+
+        contig.add_read(read_name,orientation,start_consensus)
+      end
+
+      #---------------------------------------------- BS
+      if (line =~ /^BS\s+([^\s]+)\s+([^\s]+)\s+([^\s]+)/)
+        padded_start_consensus = $1
+        padded_end_consensus = $2
+        read_name = $3
+
+        bs['padded_start_consensus'] = padded_start_consensus
+        bs['padded_end_consensus'] = padded_end_consensus
+        bs['read_name'] = read_name
+
+        read = contig.reads[read_name]
+        read.add_bs(bs)
+        bs = {}
+      end
+
+      #---------------------------------------------- RD
+      if (line =~ /^RD\s+([^\s]+)\s+([^\s]+)\s+([^\s]+)\s+([^\s]+)/)
+        read_name = $1
+        padded_bases_num = $2
+        item_num = $3
+        tag_num = $4
+        save_read_fasta = true
+
+        read = contig.reads[read_name]
+        read.add_data(padded_bases_num,item_num,tag_num)
+      end
+
+      #---------------------------------------------- QA
+      if (line =~ /^QA\s+([^\s]+)\s+([^\s]+)\s+([^\s]+)\s+([^\s]+)/)
+        qual_clip_start = $1
+        qual_clip_end = $2
+        align_clip_start = $3
+        align_clip_end = $4
+
+        read.add_qual_clipping(qual_clip_start, qual_clip_end, align_clip_start, align_clip_end)
+      end
+    end
+
+    return contig
+  end
+
+end

data/lib/scbi_ace/contig.rb

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+# Description: This class provided the methods to access to the Contig data and to add reads to the Contig
+# ---- Author: Noe Fernandez Pozo
+# ------ Date: 31-May-2011
+
+require 'read'
+
+class Contig
+	
+	attr_accessor :name,:length,:reads_num,:bs_num,:orientation,:reads,:reads_names,:fasta,:qual
+	
+	def initialize(name,length,reads_num,bs_num,orientation)
+		
+		@name = name
+		@length = length
+		@reads_num = reads_num
+		@bs_num = bs_num
+		@orientation = orientation
+		
+		@reads = {}
+		@reads_names = []
+		
+		@fasta = ''
+		@qual = ''
+	end
+	
+	def add_read(read_name,orientation,start_consensus)
+		read= Read.new(read_name,orientation,start_consensus)
+		@reads_names << read_name
+		@reads[read_name] = read
+		return read
+	end
+	
+	def add_fasta(fasta)
+		@fasta = fasta
+	end
+	
+	def add_qual(qual)
+		@qual = qual
+	end
+	
+	def get_read(read_name)
+		return @reads[read_name]
+	end
+
+	def get_read_names
+		return @reads_names
+	end
+	
+end

data/lib/scbi_ace/indexed_ace_file.rb

@@ -0,0 +1,154 @@
+
+class ContigNotFountException < RuntimeError
+end
+
+class IndexedAceFile
+
+  READ_REG_EXP=  /^([^\s]+)\s+([^\s]+)\s+([^\s]+)/
+
+  attr_reader :ace_file_name
+
+  def initialize(ace_file_name)
+    #@ace_file = File.open(ace_file_name)
+    @ace_file_name = ace_file_name
+
+    index_file_name=ace_file_name+'.scbi_index'
+
+    if !File.exists?(index_file_name)
+      create_index_file(index_file_name)
+    end
+
+    @index_file = File.open(index_file_name)
+
+  end
+
+  def self.open(ace_file_name)
+    return new(ace_file_name)
+  end
+
+  def next_contig
+    contig = nil
+
+    if !@index_file.eof?
+      line = @index_file.readline
+
+      e=line.chomp
+
+      # parse params
+      if e=~ READ_REG_EXP
+        length=$3.to_i
+        offset=$2.to_i
+
+        #puts line
+        contig = File.read(@ace_file_name,length,offset)
+      end
+    end
+    
+    return contig
+  end
+  
+
+  def each_contig
+    
+    @index_file.pos=0
+
+    begin
+      contig = next_contig
+
+      if !contig.nil?
+        yield contig
+      end
+      
+    end while !contig.nil?
+
+  end
+
+  # read a contig by its name
+  def read_contig(contig_name)
+    res = nil
+    @index_file.pos=0
+
+    @index_file.grep(/^#{contig_name}\s/) do |line|
+
+      e=line.chomp
+
+      # parse params
+      if e=~ READ_REG_EXP
+
+        #get line
+
+        length=$3.to_i #4152
+        offset=$2.to_i #3289232
+        #puts line
+        res=File.read(@ace_file_name,length,offset)
+
+      end
+
+    end
+
+    return res
+  end
+
+  def create_contig_indexes
+    res=[]
+    
+    start_pos=0
+    end_pos = 0
+    contig=nil
+    (ace_file=File.open(@ace_file_name)).grep(/^\s*CO\s/) do |line|
+      # puts ace_file.pos, line.length
+      end_pos = ace_file.pos - line.length
+
+      #puts line
+      if line=~/^\s*CO\s+([^\s]+\s)/
+
+        if contig
+          #from = last_pos if from == 0
+
+          res << "#{contig}\t#{start_pos}\t#{end_pos-start_pos}"
+
+          # puts "#{contig}\t#{start_pos}\t#{offset}"
+
+
+        end
+
+        start_pos = end_pos
+
+        contig = $1
+
+      end
+
+      #last_pos = ace_file.pos
+      #offset=last_pos - from
+    end
+
+    if contig
+      end_pos = ace_file.pos
+      res << "#{contig}\t#{start_pos}\t#{end_pos-start_pos}"
+      # puts "#{contig}\t#{start_pos}\t#{end_pos-start_pos}"
+    end
+
+
+
+    return res
+  end
+
+  def create_index_file(index_file_name)
+
+    puts "creating index file #{index_file_name}"
+
+    @index_file = File.open(index_file_name,'w+')
+    @index_file.puts(create_contig_indexes.join("\n"))
+    @index_file.close
+  end
+
+
+  def close
+    #@ace_file.close
+    @index_file.close
+  end
+
+
+
+
+end

data/lib/scbi_ace/read.rb

@@ -0,0 +1,39 @@
+# Description: This class provided the methods to add Reads data
+# ---- Author: Noe Fernandez Pozo
+# ------ Date: 31-May-2011
+
+class Read
+	
+	attr_accessor :name, :orientation, :start_in_consensus, :bs, :fasta
+	attr_accessor :padded_bases_num, :item_num, :tag_num
+	attr_accessor :qual_clip_start, :qual_clip_end, :align_clip_start, :align_clip_end
+	
+	def initialize(name,orientation,start_in_consensus)
+		@name = name
+		@orientation = orientation
+		@start_in_consensus = start_in_consensus
+		@bs = []
+	end
+	
+	def add_fasta(fasta)
+		@fasta = fasta
+	end
+	
+	def add_data(padded_bases_num,item_num,tag_num)
+		@padded_bases_num = padded_bases_num
+		@item_num = item_num
+		@tag_num = tag_num
+	end
+	
+	def add_qual_clipping(qual_clip_start, qual_clip_end, align_clip_start, align_clip_end)
+		@qual_clip_start = qual_clip_start
+		@qual_clip_end = qual_clip_end
+		@align_clip_start = align_clip_start
+		@align_clip_end = align_clip_end
+	end
+	
+	def add_bs(bs)
+		@bs.push bs
+	end
+	
+end

data/script/console

@@ -0,0 +1,10 @@
+#!/usr/bin/env ruby
+# File: script/console
+irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
+
+libs =  " -r irb/completion"
+# Perhaps use a console_lib to store any extra methods I may want available in the cosole
+# libs << " -r #{File.dirname(__FILE__) + '/../lib/console_lib/console_logger.rb'}"
+libs <<  " -r #{File.dirname(__FILE__) + '/../lib/scbi_ace.rb'}"
+puts "Loading scbi_ace gem"
+exec "#{irb} #{libs} --simple-prompt"

data/script/destroy

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/destroy'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Destroy.new.run(ARGV)

data/script/generate

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/generate'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Generate.new.run(ARGV)

data/test/test_helper.rb

@@ -0,0 +1,3 @@
+require 'stringio'
+require 'test/unit'
+require File.dirname(__FILE__) + '/../lib/scbi_ace'

data/test/test_scbi_ace.rb

@@ -0,0 +1,62 @@
+require File.dirname(__FILE__) + '/test_helper.rb'
+require 'json'
+
+class TestScbiAce < Test::Unit::TestCase
+
+  def setup
+  end
+
+  def test_open
+    ace=IndexedAceFile.new(File.join(File.dirname(__FILE__),'test.ace'))
+
+    # puts ace.read_contig('7180000000028')[0..100]
+    # puts ace.read_contig('7180000000029')
+
+    ace.close
+    assert true
+  end
+
+  def test_aceparser
+    ace=AceParser.new(File.join(File.dirname(__FILE__),'test.ace'))
+    
+    ace.each_contig do |contig|
+      
+      puts contig.reads.count
+    end
+    
+    # contig=ace.next_contig
+    
+    # puts contig.fasta
+    # ace.each_contig do |contig|
+    #
+    # end
+
+    ace.close
+
+  end
+  
+  
+  def test_next_contig
+    ace=AceParser.new(File.join(File.dirname(__FILE__),'test.ace'))
+    
+
+    
+    contig1=ace.next_contig
+    assert_equal(1701,contig1.reads.length)
+    
+    # puts JSON::pretty_generate(contig1.reads)
+        
+    contig1=ace.next_contig
+    assert_equal(3,contig1.reads.length)
+    # puts contig1.reads.first[1].fasta
+    
+    
+    contig1=ace.next_contig
+    assert_equal(4,contig1.reads.length)
+    
+    ace.close
+    
+    
+  end
+
+end

metadata

@@ -0,0 +1,83 @@
+--- !ruby/object:Gem::Specification 
+name: scbi_ace
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.0.6
+platform: ruby
+authors: 
+- Noe Fernandez & Dario Guerrero
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2012-07-25 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: hoe
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 2.8.0
+  type: :development
+  version_requirements: *id001
+description: scbi_ace is a ruby gem to read and parse ACE files containing contigs. It automatically indexes the input ace file to improve random access to contigs.
+email: 
+- noefp@uma.es , dariogf@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- History.txt
+- Manifest.txt
+- PostInstall.txt
+files: 
+- History.txt
+- Manifest.txt
+- PostInstall.txt
+- README.rdoc
+- Rakefile
+- lib/scbi_ace.rb
+- script/console
+- script/destroy
+- script/generate
+- test/test_helper.rb
+- test/test_scbi_ace.rb
+- lib/scbi_ace/indexed_ace_file.rb
+- lib/scbi_ace/ace_parser.rb
+- lib/scbi_ace/contig.rb
+- lib/scbi_ace/read.rb
+homepage: http://www.scbi.uma.es/downloads
+licenses: []
+
+post_install_message: PostInstall.txt
+rdoc_options: 
+- --main
+- README.rdoc
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+requirements: []
+
+rubyforge_project: scbi_ace
+rubygems_version: 1.8.24
+signing_key: 
+specification_version: 3
+summary: scbi_ace is a ruby gem to read and parse ACE files containing contigs
+test_files: 
+- test/test_helper.rb
+- test/test_scbi_ace.rb