quorum 0.1.0

data/lib/quorum/engine.rb

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+module Quorum
+  class Engine < Rails::Engine
+    isolate_namespace Quorum
+  end
+end

data/lib/quorum/helpers.rb

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+module Quorum
+  module Helpers
+
+    #
+    # I18n flash helper. Set flash message based on key.
+    #
+    def set_flash_message(key, kind, options = {})
+      options[:scope] = "quorum.#{controller_name}"
+      options[:scope] << ".errors" if key.to_s == "error"
+      options[:scope] << ".notices" if key.to_s == "notice"
+      options[:scope] << ".alerts" if key.to_s == "alert"
+      message = I18n.t("#{kind}", options)
+      flash[key] = message if message.present?
+    end
+ 
+  end
+end

data/lib/quorum/sequence.rb

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+module Quorum
+  module Sequence
+
+    #
+    # Create a unique hash plus timestamp.
+    #
+    def create_hash(sequence)
+      Digest::MD5.hexdigest(sequence).to_s + "-" + Time.now.to_f.to_s
+    end
+
+    #
+    # Write input sequence to file. Pass the raw input data through seqret
+    # to ensure FASTA format.
+    #
+    def write_input_sequence_to_file(tmp_dir, hash, sequence)
+      seq = File.join(tmp_dir, hash + ".seq") 
+      File.open(seq, "w") do |f|
+        f << sequence
+      end
+
+      fasta = File.join(tmp_dir, hash + ".fa")
+
+      # Force FASTA format.
+      cmd = "seqret -filter -sformat pearson -osformat fasta < #{seq} " <<
+      "> #{fasta} 2> /dev/null"
+      system(cmd)
+      if $?.exitstatus > 0
+        raise " - Please enter your sequence(s) in Plain Text as " <<
+          "FASTA."
+      end
+    end
+
+    #
+    # Discover input sequence type (nucleic acid NA or amino acid AA).
+    #
+    # Subtracting all AA single letter chars from NA single letter chars
+    # (including ALL ambiguity codes for each!) leaves us with
+    # EQILFP. If a sequence contains EQILFP, it's safe to call it an AA. 
+    #
+    # See single letter char tables for more information:
+    # http://en.wikipedia.org/wiki/Proteinogenic_amino_acid
+    # http://www.chick.manchester.ac.uk/SiteSeer/IUPAC_codes.html
+    #
+    # If a sequence doesn't contain EQILFP, it could be either an AA 
+    # or NA. To distinguish the two, count the number of As Ts Gs Cs
+    # and Ns, divide by the the length of the sequence and * 100.
+    #
+    # If the percentage of A, T, U, G, C or N is >= 15.0, call it a NA.
+    # 15% was choosen based on the data in the table 
+    # "Relative proportions (%) of bases in DNA" 
+    # (http://en.wikipedia.org/wiki/Chargaff's_rules) and the
+    # precentage of AAs found in peptides
+    # (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2590925/).
+    #
+    def discover_input_sequence_type(sequence)
+      # Index of the first newline char.
+      start = sequence.index(/\n/)
+      # Remove the sequence FASTA header.
+      seq = sequence.slice(start..-1).gsub!(/\n/, '')
+
+      if seq =~ /[EQILFP]+/
+        type = "amino_acid"
+      else
+        # Length of the sequence minus the FASTA header.
+        len = seq.length.to_f
+
+        na_percent = 15.0
+
+        a = (seq.count("A").to_f / len) * 100
+        t = (seq.count("T").to_f / len) * 100
+        u = (seq.count("U").to_f / len) * 100
+
+        g = (seq.count("G").to_f / len) * 100
+        c = (seq.count("C").to_f / len) * 100
+
+        n = (seq.count("N").to_f / len) * 100
+
+        if (a >= na_percent) || (t >= na_percent) || (u >= na_percent) || 
+          (g >= na_percent) || (c >= na_percent) || (n >= na_percent)
+          type = "nucleic_acid"
+        else
+          type = "amino_acid"
+        end
+      end
+      type
+    end
+
+  end
+end

data/lib/quorum/version.rb

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+module Quorum
+  VERSION = "0.1.0"
+end

data/lib/quorum.rb

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+require "quorum/engine"
+require "quorum/helpers"
+require "quorum/sequence"
+require "workers/quorum"
+require "resque"
+require "resque/server"
+require "net/ssh"
+
+module Quorum
+
+  ## Supported Algorithms ##
+  BLAST_ALGORITHMS = ["blastn", "blastx", "blastp", "tblastn"]
+
+  mattr_accessor :blast_remote, :blast_ssh_host, :blast_ssh_user, 
+    :blast_ssh_options, :blast_script, :blast_log_dir, :blast_tmp_dir,
+    :blast_db, :tblastn, :blastp, :blastn, :blastx, :blast_threads
+
+  class << self
+
+    ## Blast ##
+
+    # Execute remotely.
+    def blast_remote
+      @@blast_remote || false
+    end
+
+    # Net::SSH host.
+    def blast_ssh_host
+      @@blast_ssh_host || nil
+    end
+
+    # Net::SSH user.
+    def blast_ssh_user
+      @@blast_ssh_user || nil
+    end
+
+    # Net::SSH options.
+    def blast_ssh_options
+      @@blast_ssh_options || {}
+    end
+
+    # Blast script path.
+    def blast_script
+      @@blast_script || nil
+    end
+
+    # Blast log dir path.
+    def blast_log_dir
+      @@blast_log_dir || nil
+    end
+
+    # Blast tmp dir path.
+    def blast_tmp_dir
+      @@blast_tmp_dir || nil
+    end
+
+    # Blast database path.
+    def blast_db
+      @@blast_db || nil
+    end
+
+    # tblastn directories.
+    def tblastn
+      @@tblastn || []
+    end
+
+    # blastp directories.
+    def blastp
+      @@blastp || []
+    end
+
+    # blastn directories.
+    def blastn
+      @@blastn || []
+    end
+
+    # blastx directories.
+    def blastx
+      @@blastx || []
+    end
+
+    # Number of Blast threads.
+    def blast_threads
+      @@blast_threads || 1
+    end
+
+  end
+
+end

data/lib/tasks/blastdb/README

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+
+==
+
+Finished building your Blast database(s).
+
+makeblastdb results are located in quorum/log/makeblastdb.log.
+
+===================================================================
+
+Add the newly created Blast database files in
+quorum/blastdb to config/quorum_settings.yml. Update
+RAILS_ENV settings.
+
+   See config/quorum_settings.yml for instructions.
+
+===================================================================
+

data/lib/tasks/blastdb/build_blast_db.rb

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+module Quorum
+  #
+  # Build Blast Database(s)
+  #
+  class BuildBlastDB
+
+    # Valid values for @type.
+    VALID_TYPES = ["both", "prot", "nucl"]
+
+    # Blast dependencies
+    DEPENDENCIES = ["makeblastdb"]
+
+    # File bz2 and gz extensions.
+    GZIP = /\.(tgz$)|(tar.gz$)/
+    BZIP = /\.(tbz$)|(tar.bz2$)/
+
+    private
+
+    def initialize(args, output = $stdout)
+      @dir         = args[:dir]
+      @type        = args[:type]
+      @prot_file   = args[:prot_file]
+      @nucl_file   = args[:nucl_file]
+      @rebuild_db  = args[:rebuild_db]
+      @empty       = args[:empty]
+      @blastdb_dir = args[:blastdb_dir]
+      @gff_dir     = args[:gff_dir]
+      @log_dir     = args[:log_dir]
+
+      @output = output
+    end
+
+    #
+    # Check build_blast_db dependencies.
+    #
+    def check_dependencies
+      DEPENDENCIES.each do |b|
+        system("which #{b} > /dev/null 2>&1")
+        if $?.exitstatus > 0
+          raise "Dependency not found. Please add `#{b}` to your PATH."
+        end
+      end
+    end
+
+    #
+    # Make Quorum directories.
+    #
+    def make_directories
+      begin
+        `rm -rf #{@blastdb_dir}` if File.directory?(@blastdb_dir) && @rebuild_db
+        Dir.mkdir(@blastdb_dir) unless File.directory?(@blastdb_dir)
+
+        `rm -rf #{@gff_dir}` if File.directory?(@gff_dir) && @rebuild_db
+        Dir.mkdir(@gff_dir) unless File.directory?(@gff_dir)
+
+        Dir.mkdir(@log_dir) unless File.directory?(@log_dir)
+      rescue SystemCallError => e
+        @output.puts e.message
+        raise "Unable to make directory. " << 
+          "Perhaps you forgot to execute the quorum initializer. \n\n" <<
+          "rails generate quorum:install"
+      end
+    end
+
+    #
+    # Create directories per tarball and return tarball file name 
+    # minus the file extension.
+    #
+    def create_file_name(file, base_dir)
+      file_name = file.split("/").delete_if { |f| f.include?(".") }.first
+      unless File.exists?(File.join(base_dir, file_name))
+        Dir.mkdir(File.join(base_dir, file_name))
+      end
+      file_name
+    end
+
+    #
+    # Extracts and concatenates files from tarballs.
+    #
+    def extract_files(src, file, flag, path)
+      extract_data_error = File.join(@log_dir, "extract_data_error.log")
+
+      cmd = "tar -x#{flag}Of #{src} #{file} >> #{path} 2>> " <<
+        "#{extract_data_error}"
+      system(cmd)
+      if $?.exitstatus > 0
+        raise "Data extraction error. " <<
+          "See #{extract_data_error} for details."
+      end
+    end
+
+    #
+    # Execute makeblastdb on an extracted dataset.
+    #
+    def execute_makeblastdb(type, title, input)
+      @output.puts "Executing makeblastdb for #{title} dbtype #{type}..."
+
+      makeblast_log = File.join(@log_dir, "makeblastdb.log")
+      output        = File.dirname(input)
+
+      cmd = "makeblastdb " <<
+        "-dbtype #{type} " <<
+        "-title #{title} " <<
+        "-in #{input} " <<
+        "-out #{output} " <<
+        "-hash_index >> #{makeblast_log}"
+      system(cmd)
+      if $?.exitstatus > 0
+        raise "makeblastdb error. " <<
+          "See #{makeblast_log} for details."
+      end
+    end
+
+    #
+    # Builds a Blast database from parse_blast_db_data.
+    #
+    def build_blast_db(blastdb)
+      Dir.glob(File.expand_path(blastdb) + "/*").each do |d|
+        if File.directory?(d)
+          contigs  = File.join(d, "contigs.fa")
+          peptides = File.join(d, "peptides.fa")
+
+          found = false 
+
+          if File.exists?(contigs) && File.readable?(contigs)
+            execute_makeblastdb("nucl", d, contigs)
+            found = true
+          end
+          if File.exists?(peptides) && File.readable?(peptides)
+            execute_makeblastdb("prot", d, peptides)
+            found = true
+          end
+
+          unless found
+            raise "Extracted data not found for #{contigs} or #{peptides}. " <<
+            "Make sure you supplied the correct data directory and file names."
+          end
+        end
+      end
+    end
+
+    #
+    # Display BLAST_README
+    #
+    def readme
+      file = File.readlines(File.join(File.dirname(__FILE__), "README"))
+      file.each { |f| @output.print f }
+    end
+
+    public
+
+    #
+    # Parse Blast database data.
+    #
+    def build_blast_db_data
+      # Create necessary directories and return.
+      if @empty
+        make_directories
+        return
+      end
+
+      if @dir.blank?
+        raise "DIR must be set to continue. Execute `rake -D` for more information."
+      end
+
+      unless VALID_TYPES.include?(@type)
+        raise "Unknown type: #{@type}. " << 
+          "Please provide one: both, nucl or prot."
+      end
+
+      check_dependencies
+
+      make_directories
+
+      begin
+        @dir.split(':').each do |d|
+          unless File.directory?(d)    
+            raise "Directory not found: #{d}"
+          end
+
+          @data = Dir.glob("#{d}/*.{tgz,tar.gz,tbz,tar.bz2}")
+
+          if @data.blank?
+            raise "Data not found. Please check your directory and try " <<
+            "again.\nDirectory Entered: #{d}"
+          end
+
+          @data.each do |s|
+            if s =~ GZIP
+              files = `tar -tzf #{s}` 
+              flag  = "z"
+            elsif s =~ BZIP
+              files = `tar -tjf #{s}`
+              flag  = "j"       
+            end
+            files = files.split(/\n/)
+            files.each do |f|
+              if f.include?(@prot_file)
+                file_name = create_file_name(f, @blastdb_dir)
+                extract_files(s, f, flag, File.join(@blastdb_dir, file_name, "peptides.fa"))
+              elsif f.include?(@nucl_file)
+                file_name = create_file_name(f, @blastdb_dir)
+                extract_files(s, f, flag, File.join(@blastdb_dir, file_name, "contigs.fa"))
+              elsif f.include?("gff")
+                file_name = create_file_name(f, @gff_dir)
+                extract_files(s, f, flag, File.join(@gff_dir, file_name, "annots.gff"))
+              end
+            end
+          end
+        end
+        build_blast_db(@blastdb_dir)
+      rescue Exception => e
+        # Remove empty directories.
+        `rm -rf #{@blastdb_dir}/*` if File.directory?(@blastdb_dir)
+        `rm -rf #{@gff_dir}/*` if File.directory?(@gff_dir)
+        raise e
+      end
+      readme
+    end
+
+  end
+end

data/lib/tasks/quorum_resque.rake

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+require 'resque/tasks'
+
+task "resque:setup" => :environment

data/lib/tasks/quorum_tasks.rake

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+#
+# Quourm Rake Tasks
+#
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), 'blastdb'))
+
+require 'build_blast_db'
+
+namespace :quorum do
+  namespace :blastdb do
+    desc "Build Blast Database (options: DIR=/path/to/data " << 
+    "{valid extensions: .tar.gz .tgz .tar.bz2 .tbz} " << 
+    "-- separate multiple directories with a colon. " << 
+    "TYPE={both}{prot}{nucl} -- defaults to both. " << 
+    "PROT_FILE_NAME= -- defaults to peptides.fa. " <<
+    "NUCL_FILE_NAME= -- defaults to contigs.fa. " <<
+    "REBUILD_DB= {true or false} -- remove existing blast database(s). " <<
+    "Defaults to false. " <<
+    "EMPTY={true or false} -- skip makeblastdb and create empty " <<
+    "directories. Use this option if you prefer to create your own " <<
+    "Blast database. Defaults to false.)"
+    task :build do
+
+      args = {}
+
+      args[:dir]        = ENV['DIR']
+      args[:type]       = ENV['TYPE'] || 'both'
+      args[:prot_file]  = ENV['PROT_FILE_NAME'] || 'peptides.fa'
+      args[:nucl_file]  = ENV['NUCL_FILE_NAME'] || 'contigs.fa'
+      args[:rebuild_db] = ENV['REBUILD_DB'] || false
+      args[:empty]      = ENV['EMPTY'] || false
+
+      args[:blastdb_dir] = File.join(::Rails.root.to_s, "quorum", "blastdb")
+      args[:gff_dir]     = File.join(::Rails.root.to_s, "quorum", "gff3")
+      args[:log_dir]     = File.join(::Rails.root.to_s, "quorum", "log")
+
+      args[:type]      = args[:type].downcase.strip
+      args[:prot_file] = args[:prot_file].downcase.strip
+      args[:nucl_file] = args[:nucl_file].downcase.strip
+      args[:nucl_file] = "NULL" if args[:type] == "prot"
+      args[:prot_file] = "NULL" if args[:type] == "nucl"
+      
+      puts "Building your Blast database(s). This may take a while..."
+      
+      build = Quorum::BuildBlastDB.new(args)
+      build.build_blast_db_data
+    end
+  end
+end
+

data/lib/workers/quorum.rb

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+module Workers 
+  class System
+    @queue = :system_queue
+
+    #
+    # Resque worker method.
+    #
+    def self.perform(cmd, remote, ssh_host, ssh_user, ssh_options = {})
+      unless ssh_options.empty?
+        # Convert each key in ssh_options to a symbol.
+        ssh_options = ssh_options.inject({}) do |memo, (k, v)|
+          memo[k.to_sym] = v
+        memo
+        end
+      end
+
+      exit_status = 1
+
+      if remote
+        # Execute command on remote machine.
+        Net::SSH.start(ssh_host, ssh_user, ssh_options) do |ssh|
+          ssh.open_channel do |ch|
+            ch.exec(cmd) do |ch, success|
+              unless success 
+                Rails.logger.warn "Channel Net::SSH exec() failed. :'("
+              else
+                # Read the exit status of the remote process.
+                ch.on_request("exit-status") do |ch, data|
+                  exit_status = data.read_long
+                end
+              end
+            end
+          end
+          ssh.loop
+        end
+      else
+        system(cmd)
+        exit_status = $?.exitstatus
+      end
+      if exit_status > 0
+        raise "Worker failed :'(. See quorum/log/quorum.log for more information."
+      end
+    end
+  end
+end

data/quorum.gemspec

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+$:.push File.expand_path("../lib", __FILE__)
+
+# Maintain your gem's version:
+require "quorum/version"
+
+# Describe your gem and declare its dependencies:
+Gem::Specification.new do |s|
+  s.name        = "quorum"
+  s.version     = Quorum::VERSION
+  s.authors     = ["Ken Seal"]
+  s.email       = ["kas@ncgr.org"]
+  s.homepage    = "https://github.com/ncgr/quorum"
+  s.summary     = "Flexible bioinformatics search tool."
+  s.description = "Flexible bioinformatics search tool."
+
+  s.files = `git ls-files`.split(/\n/) 
+
+  s.add_dependency "rails", "~> 3.1.0"
+  s.add_dependency "jquery-rails"
+  s.add_dependency "net-ssh", "~> 2.2.1"
+  s.add_dependency "resque", "~> 1.19.0"
+  s.add_dependency "bio-blastxmlparser", "~> 1.0.1"
+
+  s.add_development_dependency "mysql2"
+  s.add_development_dependency "rspec-rails", "~> 2.6"
+  s.add_development_dependency "capybara"
+  s.add_development_dependency "database_cleaner"
+  s.add_development_dependency "factory_girl_rails", "~> 1.2.0"
+end

data/script/rails

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+#!/usr/bin/env ruby
+#!/usr/bin/env ruby
+# This command will automatically be run when you run "rails" with Rails 3 gems installed from the root of your application.
+
+ENGINE_PATH = File.expand_path('../..',  __FILE__)
+load File.expand_path('../../spec/dummy/script/rails',  __FILE__)

data/spec/data/nucl_prot_seqs.txt

@@ -0,0 +1,36 @@
+>TOG900080
+TGATAGGATAATTCTAGACAAAACATTAGCCGATCAAGTGTCATCATGGAAAAGCAGCAGGGGCCTTAGTGATACAGTGGTGACTGATCATGCTTGTTCTGGGGAAACATGCTCGTACTACGCAATTGGAGATGTATTTATTTGTGAAAAGACTGGACAAGTTCATGTTTGTGACGAAACATGTAGGGAAGTAGTAATGGATCCCACCAACGAGCTTTTGGTCTGTACAATATCTGGCCACTGTTTTGACAGATTGCTATCACCTGCTGAAATGGAGCCTGATGCTGAGCAGCAGCAAGGTGGTGCGGCAGATGAGGCAGAACCGTTTATGGGATCTGGCCGTTTTGCACGGGCTTATTTGCTGGGATACAATTGTGCTGATGAAAAGGAGCTTGAAGCTACTTTGAGGTTTTGCTGATCCCTATTGGCCCTTCTGGAGTGGATGATCTCATGTCTCAGCATTTACCTATTTAAGATCAAATAAATCGGGTTTCCTTTTCGTGTTTCTCTTGGCATAAGAATGTTTGATTAGATCTAGATTATGAAACTCTAATCGTCTTCTATATTAATAATTGTATGCTTAAATTTATAGTTGAAATTCCATTGATGAATTTTTCTT
+>TOG899661
+CAGAAGACATGTCTTTGACAAAGGTATACCATCTTTTCCNCCAACTTGGTTTGAGACATTTATTTGTTGTACCTCGTCCATCGCGTGTGCTTGGTTTGATAACCAGAAAAGATTTGTTGATTGAGGACACAGATGCGAATACATTAGAGCTTCAGGCAACTAGTAGTTCGGCATCCAGGTAAAAGATTGATGGCAAGGAATGCAGATGTGGAGAGCCCTCTGCTAAATGGTCTTCTGGTTCAGAATCAGATACCTGACTAATACCGTCTGCAGCCTTCCCGAATTCCTTTTTGCGTCCCATTTTCACTTGAAAATCATTCTTTATTATTTTTGTATTAATGTTGAAATAGGTTAGAGAACCCGATATTTTGGGGATGGAACGGGGTTGTAGACTGACAGTATACCCTAGAATTTTGTATATAAAGTATAAACTACAGCAAGCACAGAAAAAAATCATGAAAGCGCCCTTGTGATAATTATGATAGCAGAATTTAGACTGAT
+>TOG899078
+CTCTCTCTCTCTCTCTCTCTCTCTCTCTCCGTCGTCGTTTTGGGTTCTGCGGATCGGTGGATTCTGGTCGCGAATTCCGACGCTGTTCGTGGCGGCGAACCGAATTCCGGTCAACAAGCGAAGAAGATGAAGGTTTTCGTCAAGACTCTGAAGGGCTCTCACTTCGAAATCGAAGTCAAGCCCCAAGACACGGTTTCGGATGTGAAGAAAAATATTGAAACTGTTCAAGGTGGATGTCTATCCTGCCGCGCAGCAAATGCTTATTCATCAAGGGAAAGTTCTTAAGGATGGTACTACCTTGGAGGAAAATAAAGTAGCTGAAAATAGTTTCATTGTGATTATGATTTCCAAGAGTAAGACTCCGTCTGGTGAAGGATCTACTACTTCAGCTGCACCTTCAGCTAAGGCTCCAGCTCCTGCTCCTATATCTTCGGGCACGGCTGTGGAAGGTTCTGATGTCTATGGACAAGCAGCATCCAATCTGGTTGCTGGTAGCAACTTGGAAGACACAATTCAGCAAATTCTTGATGTTGGAGGAGGGACCTGGGATAGGGATACTGTAGTCCGGGCTCTTCGAGCTGCCTTCAACAACCCTGAGAGAGCTATTGAATATTTATATTCAGGAATCCCCGAGCAAGCTGAAGCTCCACCTGTGGGCCGTGTGCCTGCAAGTGCACAACCTGCAAATCCTCCAGCAGCTGCAGCTCCGCAAGCGGCACAACCTGCTCCTGTTACCTCAAGTGGGCCTAATGCTAATCCTTTAGACCTTTTTCCACAGGGCCTCCCAAATGTTGGTTCTGGTGGTGCTGGTGCTGGTGCTGGCTCTTTAGATTTTCTTCGCAACAGCCAACAATTCCAAGCCTTGCGAGCTATGGTGCAGGCTAATCCACAAATATTGCAGCCTATGCTACAAGAGCTTGGCAAACAGAATCCTCATCTAATGAGATTGATTCGAGATCATCAAGCTGACTTCCTTCGCTTGATAAATGAGCCTGTGGAAGGTGGCGAAGGGAACCCATTGGGGCAGCTGGCTGGTGGCATACCACAAGCAATAACTGTCACCCCTGAGGAGCGCCAAGCAATTGAACGTCTTGAAGCAATGGGTTTCGATCGTGCGATTGTATTGGAGGTGTTCTTCGCTTGCAACAAAAATGAGGAATTGGCTGCCAACTACCTTTTAGATCACATGCATGAGTTCGACGAACAATAAATCTCTTCATGTTGCTAAATTATTTATCTGTTATCTTTTTAATGTTTATGGGGCCTTTGTTTTACTAGACGGTTTGATGAGGTAATACTTGAAAATGAAAAAAATCTCAAGTGGAGAAGGAACGTTTTTACCACCTCCACATTATTGCCTTTGTGGACAGTCTCAGTATTCATATACATAGTCGTTTGTCCTGTACTATTGGTATTGTGCATCCTTTTAACATGTGTAATTGTTTAGCTGCGCATCCTATTCTATATTTTCT
+>TOG896930
+CGTTCGCATTGTTCACTCACCATACGCACTTCCATTTTCATCTCCCACCGTCGCATTTTCTTCGGATCTGAAATTCCTCACCATGAATCGCCACCACGATCCCAATCCATTCGACGAAGACGAAGTCAATCCCTTCTCGAACGGTGCTGCTCCTGGATCTAAATCACGTATTCCACCATTGGCATCCGAACCACTGGGCTTTGGTCAAAGACATGATGCTACAGTTGATATTCCTTTGGATACCACAAATGAGCCTAAAAAAAAAGGTCAAGAGCTAGCAGCTTGGGAAGCAGATTTGAAAAGGAGAGAAAAGGATTTAAAAAGAAGAGAGGATGCTGTTTCTAGAGCTGGTGTGCCTGTTGATGATAAGAATTGGCCTCCGATTTTCCCAATTATTCACCATGATATTGCCAATGAGATACCGGTTCATGCTCAGAGGCTGCAATATTTGGCCTTTGCAAGTTGGTTAGGAATTGTTCTCTGCCTTGTTTTTAATGTAGTTGCTGTGATGGTCTGTTGGATCAGAGGCGGTGGTGTTAAAATTTTTTTCCTTGCGGTGATCTATGCTCTACTTGGTGTTCCCCTTTCATATGTGCTTTGGTACAGGCCCCTTTATCGTGCTATGAGGACGGATAGTGCACTGAAGTTTGGCTGGTTTTTCATGTTCTACTTGCTTCATATTGCATTTTGCATCTTTGCTGCAATTGCACCTCCAGTTGTTTTTCATGGGAAATCATTAACGGGCATCCTTGCAGCAACTGACGTCTTCTCAGACCATGTATTGGTTGGGATATTCTATTTGGTTGGATTTGGCCTGTTTTGCTTGGAGTCTCTTCTAAGCTTGTGGGTAATTCAGAAAATATACCTGTTTTTCCGGGGGCATAAGTGAGGCTACTCAGGATTTTGATCCATCGGCTTTTATGATATCAGTCACTTCCCGGCGTGGCTTAGTATATTCTTTCTTTTTGTCTATCCTCTTTTTTCGCTTGCAATATTTTCGTGTGATATTGTTTGTTGTTGTAGTCTAGTTCTTGTTACAGAGCTTAGTGTGTAATTTCCTGTGTAATGAATTCTGTGAAGTTTAGTAATTTTCTAGTGTAACAATAACCAAGCTTTGCTTTCGATAAGCATATATGTAGTGGATTTCCATAAGGAATTATTGTAGTGCTATTGTAGTTGTGAATAGTGACACCCCTCGGAGGTTTTCTATTTGTAAGACAGCACTGATGCAAACACTTTAGTTAAAATTCATGTAGGATCTATTCAATT
+>TOG902802
+CAGGATACACCTCCAGATGGGGAAAATATGACAGGAGCCTCCAAAGAGATGAATGTAGAATCTATTCCTTCCTTCTTTCAAGATATTATTGAGCGTATGGTTTCCTCACAAGTTATGACTGTGAAGCCTGATGCTTGCATTGTGGATTTCTATAATGAGGGCGATCACTCACATCCCTACAATTGGCCACATTGGTATGGAAGGCCTGTCTATATCCTTTCCCTGACAGAATGTGATATGACTTTAGGAAGAGTAATTTCCTCAGACCATCCAGGGGATTACAGGGGCTCTCTGAAGCTTTCTCTTCTCCCTGGGTCTCTTCTGTCAAGGCAAGGGAAATCTACTAATTTTGCTAGATATGCTATTCCTTCTATCCGCAAACAACGCATACTTGTTATTTTTACAAAGTCCCAACCAAAGAAGTCACTGTCAAGTGATGCTCAACGTTTTACCTCATCAGCAGCATCTTCTCATTGGGGTCCACCGCCAAGCCGTTCCCCCAATCACGTTCGTCATCATTTAGGCCACAAGCATTATGCTTCAGCTCCAACAAACGGAGGACTGCCAGCTCCACCAATCCGGCCACA
+>TOG913027
+AAGGACTAGTTGATTTGCTACATGTGTTCTGTGTTGTTCTTGCTTTGGTAAATGTGTCTCTAGTGAAAGCAGAAGATCCATACAAGTTCTACACATGGACAGTGACTTATGGAACTCTTTCTCCTCTGGGCAGTCCTCAACAAGTTATTCTGATCAATGGTCAGTTTCCTGGTCCAAGACTTGACTTGGTAACTAATGACAACGTGATTCTCAACCTCATCAACAAGCTGGATGAGCCATTCTTGCTCACATGGAATGGCATTAAGCAGAGGAAAAATTCTTGGCAAGATGGGGTTTTAGGAACTAACTGTCCCATTCCTCCAAACTCAAATTACACTTACAAGTTTCAGGCCAAGGATCAGATTGGCACTTATACATACTTTCCATCAACTAAGATGCATAAAGCTTCTGGAGGGTTTGGAGCTCTCAATGTTCTTCATAGATCTGTCATCCCAATCCCTTATCCAAACCCTGATGGAGATTTTACATTACTCATTGGTGATTGGTACAAAACTAGCCACAAGACATTAAGCCAAACATTGGATTCTGGGAAATCTCTTGCCTTTCCTGATGGCCTCCTTATCAATGGCCAGGCTCATTCTACCTTCACTGTTAACCAGGGAAAAACCTATATGTTCAGGATCTCAAATGTTGGTCTGTCAACCTCAATTAACTTCAGAATTCAGGGACATACCCTAAAACTAGTTGAGGTTGAAGGATCACACACTATCCAGAACGAATACGACTCGCTTGATGTGCATGTTGGCCAATCAGTTTCTGTGTTAGTAACCTTAAATCAACCTCCAAAGGACTATTACATCGTTGCCTCAACAAGATTTACCAAGACTGTTCTCACTACAACCTCAGTGCTACACTAAAATTCTCAGTCAGCCGCATCAGGATCCTTGCCTGCTCCCCCTGCTGACAAT
+>TOG919655
+ATTGAAATACGTCTTGCAAAAGCTGAAGCTATTAATTGGACATCTCTCGAATATAGCAAGGATATGCCTCCCCAAAAAATTAAAGTGCCTACAATTCAATCTGAAAGGCCTGCATACCCATCATCAAAGCCAAGGACAAAAGATTGGGATAAGTTGGAAGCTATGGTGAAAAAAGAGGAGAAAGAAGAAAAGCTGGATGGTGATGCTGCTTTGAATAAATTGTTCCGTGATATTTATCAAAATGCTGATGAGGACATGCGGAGAGCAATGAGCAAGTCATTTCTGGAGTCAAATGGAACAGTGCTGTCAACGGATTGGAAAGAAGTGGGATCCAAGAAGGTGGAAGGAAGTCCTCCAGAAGGTATGGAATTGAAGAAATGGGAGTACTAATTCAGTACAAGCTGATGCTCATGAGAGTTCAAATTCACAAAAATAAATTCTGAGAAGGGAAACAAATTCTGTAATCTTAATGGTATCGGTTATTTTG
+>TOG906701
+TGAGATCATGCGCGAAATGATGAGGAATACAGACAGAGCCATGAGCAACATTGAGTCTTCTCCTGAGGGATTCAACATGCTGAGGCGCATGTATGAAAATGTTCAAGAACCATTTTTAAATGCCACTACAATGGCTGGTAATACAGGAAATGATGGTGTCAGGAATCAATCAACTAATCCCTCAACGACTAATTCTGAAGCAACTTCCCCTGTTCCAAATACTAACCCACTTCCTAATCCTTGGTCCTCCACTGGAACTGGAGGTGCACAAGGCAACACCAGAAGGACAACTGCTGGTGGGGATGCTCGGCAGCAGGCACTCACTGGACTAGGAGGACTTGGTGTGCCAGATCTTGAAGGCATGATGGGTGGTATGCCAGATCCTGCTATGTTGACCCAATTAATGCAAAATCCAGCTATTTCACAAATGATGCAGAGTATCCTTTCCAATCCACAGACTATGAATCAGATTCTTGGTCTCAATACTGAGCAGCGTGGCATGCCTGATCTAAACTCACTAAGAAGATGTGATGCAAAACCCAGAGTTTCTTCGCTTATTTTCCTCACCTGAGACACTGCAGCAACTCATGTCTTTCCAGCAATCTCTTATGTCTCAAGTTGG
+>TOG894885
+CAGCTCTATTCTCCACCAACACAAAAACGCTCACAAACTAGCTTCTTTGGAGAAAACATTAGAGACAATAGTGGCGGTGGTGGGAACAATGGCAGCCTCACTACAAGCAGCAGCTACTTTCATGCAACCAACCAAGTTTGGTCGCACCAACACTTTGCAGCTGAAATCTACTCAATCCATTTCTAAGGCTTTTGGGTTGGAGCCCTCTGCAGCTAAGGTCTCATGTTCCCTTCAGGCTGATTTCAAGGAGTTGGCTCACAAGTGTGTTGAAGCTACCAAGATTGCTGGGTTTGCTCTTGCCACCTCTGCTCTAGTTGTCTCTGGAGCAAGTGCGGAAGGTGCTCCGAAGAGGCTAACCTTCGATGAAATCCAGAGCAAGACATACATGGAAGTGAAGGGAACCGGAACCGCAAACCAGTGCCCCACCATTGAAGGGGGAGTGGAATCATTTTCCTTCAAGGCCGGGAAGTACAATGCCAAGAAGTTCTGCCTTGAACCCACTTCATTCACAGTGAAGGCAGAGGGAGTAGCCAAGAACGCCCCACTTGAGTTCCAAAACACCAAGCTCATGACACGTCTGACCTACACCCTCGACGAGATCGAAGGACCCTTTGAGGTTTCCTCTGATGGCACTGTCAAGTTCGAGGAGAAAGATGGCATTGACTACGCTGCTGTCACAGTTCAGCTTCCCGGTGGCGAGCGTGTTCCATTCCTTTTCACCATCAAACAGTTGGTAGCATCTGGGAAGCCAGACAGCTTCAGTGGGGAGTTTCTAGTGCCTTCATACCGTGGATCTTCCTTCTTGGACCCCAAGGGAAGAGGTGCGTCAACTGGTTATGACAATGCTGTCGCATTGCCTGCTGGTGGCAGAGGAGATGAGGAAGAACTTGCTAAGGAGAACAACCAGAGTGCTTCTTCATCCCAAGGGAAGATCACCTTGAGCGTGACACAGAGCAAGCCTGATACCGGTGAGGTGATTGGTGTGTTCGAGAGCATTCAGCCGTCCGACACTGATTTGGGAGCGAAAGCTCCCAAGGATGTGAAGATCCAGGGAGTTTGGTATGCTCAGCTCGAGTCATAGACAGCTTTATCTCTCTTCTGCTTTATTTTGTATTTTGTTGTAACTTCTCAGTGTTGCTGCCATTACCTTTGACACCACTGTCCCAGCATGAGAGTGTTATCCTTGTTTGTATGTATACTATCGACTTTCAATTATAATGCTCGAAAATGTCCAAGGTTT
+>TOG897619
+AGCAGTGTTCCCATGAAACCTTCCCACTGAGTCAACTCACTCTGTACATAAAACCCTCTTCATCATCATCATGGCTTCTCAAGTTTTTCTTCAGCAAGGGTTGTTACTGTTTGCCCCAAACCAATGTTCTCCAACCAAGCTCGGTGTATCTTCTTGCCTCGGTTCTCGTAACTTTCCGTTGATTTCCTCCACCTCAATTTCATGGCGTTGCAACAACCCTCTCTCTGCCAAACCCTCTTTTGTTGTCAGAGCTGACTCCAATGTCGACGCTGCTTCCGACAATGCTGGTGAAGTTCCAGAAGCTGAAGGTAGCGTTGATCAGGTTCCTGAAGATGGAGAAGCAGAACTAGCTTCGGATTCTGAGGTGGAGCAACCCAAGCCCCCTAGAAAGCAACGAGTCAAGCTTGGAGATGTTATGGGGATATTGAATCAGAGGGCAATTGAGGCATCGGAAAGCATGAGGCCGACTCCAGAAATTAGGACTGGAGATGTTGTGGAAATCAAACTGGAAGTTCCTGAGAACAAGCGTAGGTTGTCTATTTATAAAGGTATAGTCATCTCAAGACAAAATGCTGGTATTCACACAACTATTCGAATCCGAAGGATTATTGCTGGCACAGGGGTTGAGATTGTCTTCCCAATTTACTCACCAAACATCAAAGAAATCAAAGTGGTAAACCACCGTAAAGTCAGAAGAGCAAGATTGTACTATTTAAGAGACAAGCTTCCCAGATTCTCCACTTTCAAATGATACGGTTACCACTTCTCATCCTGATCTTCTTCAAAGTAGTTGCTGATATTGCAGGGCCATATTTTGGTTATTTCGTTTTGTTGTGTTGTAGAATATATCATTTTTCTTCCTCTAAATCTATCCTCCGAGAATTGGAAACAAGTGTATGTATGTTGCCCTTGATAATATTTGAAATTTGAAGTGTTCTCCCTTGCATTCCTTGGTATAGGATAGAAAGCCAAGCTCCTAAACAAACATTACTAAATATGACAGTCTAAGGAATGAGCATGTGTATCGATACCAGTTAAGTGCATTGTGAATGTATTTTTTTTTTTTATCTCTATCCATAAAAAAAGGTATGTTCATTCTTG
+>TOG898302
+AAGAAACAAGAGAGAGAAGATGATTTAGATGAGCCAAAAACAAAGGAAAAACGGCAAAAGGGAGAGAAAGGAAAATCTCCATCAGGTTTTCTTGCTCCTCTCCAGCTATCTGATGCCCTTGTAAACTTCCTTGGTACTGGAGAAAGTGAATTATCAAGATCTGATGTCATAAAAAGAATGTGGGAATACATAAAAGGAAACGACCTTCAGGATCCTTCTGACAAGAGGAAAATATTATGCGACGACAAGCTGAAAGAACTCTTTGATGTGGACTCCTTTAACGGCTTCACCGTTACAAAACTGTTGACTCCTCATTTTATAAAGGCAGAGCAGTGAGTTGCTTGTGGAAATCGGTAATGTTGTCCAATTAGGTTTGGAAGGTCCTTCTTTTGTGGCCTTTTGGCATTGTCTGCCAACACGAGGAATAGGAATTAGGAACATGACAGATTTTCAGTAAATTTTTCTCCAAGAATTTAATGTTACGTGACCATTACTTTGTTTTTTTTAATATCACGTTTTGTCACTTGGCAGTTGAAATTTTTGTATATTTTCAGTTCCTGAAGCTGCAAGGATAATGCTGACTTCTTACTCTACTCTGCATTTGCTCATATGAGGCACTACACATATCCATAATACATGAATAAATTTGCAGTATTGAA
+>TOG897516
+CATTTGTTCCATTTGCTCAGGCATTTGCAGCTGTACTTACAGCTGTCCTTACTGGTTCTCTCTATTATGTGGCTGCCTCTCCTAAAGATCCTACTTATATTGTGGCACCTGTTTTACAGTCTCGCTCTGGTCGTCAAGATTTGAAAAAGCTATTTGAAGCCTGGTATGAGAAACGGCAAATGAAAAAAATATATTCACCACTTCTGGAAGGACTACTAGCTCTCTACCTAGGATTTGAGTGGATCCAAACGAATAACATTCTTGCTCCCATTATCACACATGGCATATACTCCACAGTTATATTGGGACATGGCCTTTGGAAGATAAACGACCACCGGCGAAGACTACGTCAAAGAATCCAACAGCTCAAATCTGAAGAACAAAATTCCCAGTAGACTTTGAAATACCTTCCATGTCTGGCTGTGATACAAAAAATGTATATGTATGTATTAGAGCTGCTAATTATGTAAAGAGAAAAGATGTATATACTTGTGTTAGCTGAGGTCTCGTACACACTGAATATTCAGGTTTTGTTCACCATTTTCTAATTTCGAGTTACTATATGTAGTGTTTTCTAATAAAATGAAATAAAATCCCCAAGTTGGGTTGATTTAAATT
+>TOG894063
+GAGACCTGTTATGATTCACAGAGCCATTCTAGGATCTGTTGAGCGCATGTTTGCCATTCTTTTAGAGCACTACAAGGGTAAATGGCCCTTGTGGCTCAGTCCTCGTCAAGCAATTGTATGTCCTGTGTCAGAGAAATCACAAGCTTATGCACTGCAGGTGCGAGATCAGATCCACCAAGCAGGATATCACGTTGATGCTGATACAACTGATCGGAAGATTCAGAAGAAGGTACGGGAAGCTCAATTAGCGCAGTACAACTACATCTTGGTTGTTGGAGAGGAGGAAGCTAATACAGGACAGGTGAGTGTACGGGTTAGAGATAAAGCAGACCATAGCGTTATGAGTATTGAGAATCTACTCAAACACTTCAGCGACGAAGTTGCAGCTTTTCATTGATACTTCTCTTGTGAAAACTGTTGGAAGCAAATTTTACCCCCACTCACCTAGTTTGTTCACACTTTGTGTGCATTATTTATATTTTCAGCCTGACAATTTACATTTAGATGATTTGGGTAATGACTGTATTTTCTATGTGAATTTTGGAGCGCACTGATATCGATCCATTGTTTGAAAAGCTGAGAGAAAGTGTAATCTTTTATTTTCTGTCTACATTTTAATTATGTTTTTCGTTAGTTTTTTCCTTTTATATATTTGTTTGTTAAATTGAAGGAAACTATTGTTGG
+>TOG897346
+GGCACCAGGGATCTTACAAGGCTGGATCTCCATAATAACAAGTTGACAGGGCCTATTCCTCCTCAAATTGGACGGTTGAAGCGTCTTAAAATACTCAATTTGAGGTGGAACAAACTACAGGATGCAATTCCTCCAGAAATTGGCGAGCTTAAAAGTTTAACACATCTGTACCTAAGCTTCAATAGTTTCAAGGGAGAAATTCCCAAAGAGCTAGCAAATCTTCCAGACCTTCGCTACCTTTATCTTCATGAAAACCGTTTAATTGGTAGGATACCACCTGAGTTGGGCACTCTACAAAACCTTCGGCACTTGGATGCTGGTAACAATCATTTGGTGGGTACCATAAGGGAACTCATTCGTATTGAAGGTTGCTTTCCAGCACTCCGCAATCTATATCTAAACAATAATTATTTTACTGGAGGAATGCCTGCACAACTTGCCAACTTATCCAGTCTTGAGATCTTGTACCTGTCCTACAATAAAATGTCAGGAGTTATACCATCTAGCCTTGCTCATATTCCTAAATTGACATACTTGTACTTGGATCACAATCAGTTTTCGGGGAGAATTCCCGAACCCTTTTACAAACATTCATTTTTGAAAGAAATGTACATCGAGGGAAATGCATTCCGGCCTGGTGTTAAACCCATTGGTTTCCATAAAGTGCTTGAAGTTTCTGATTCAGACTTCCTTGTTTAATGAAACTCAACATATTTAGTTTTTTAGGAAGTTTACGTGTATAATTAATGAAACAATAGCTCCTCTGATTTTCTCAATGAAAATTGCTATATGGGTAATTCAATTTTTGTCACGGCTGTCTTGTCAGAAGAATCAATAAATAATAGTGTTTTTTAACTCT
+>TOG915900
+GGAAATGAGCACAATGTTAAGCAGATCAAGAATTACCGCCAAAAGGTTGAGGAGGAACTCTCCAAAATTTGTGGTGACATCCTGACTATTATAGACCAGCATCTAATTCCTTCTTCCGCCTCAGCAGAAGCTAGTGTTTTCTACTATAAGATGAAAGGTGATTATTATCGGTATCTTGCTGAGTTCAAGACCGACCAAGAAAGGAAAGAGGCAGCCGAGCAGTCACTCAAGGGATATGAGGCTGCTTCAGCCACTGCCAACACCGATCTTCCATCAACACATCCAATCCGTCTTGGACTTGCTCTCAACTTCTCTGTCTTTTATTACGAGATCATGAACTCTCCTGAAAGGGCCTGCCATTTGGCTAAACAAGCTTTTGATGAGGCAATTGCAGAGTTGGACACCTTGAGTGAAGAGTCATACAAGGACAGTACTTTGATCATGCAGTTGTTGAGAGACAACCTGACTCTCTGGACATCCGATTTGCCAGAAGATGGAGGCGAGGAGAACATAAAAGCTGAAGAAGCCAAACCTACTGAGCCTGAGAATTAACTAGGTTCTTTTGGATCTTTGGCCCTGATTCAATAGTCAGATTTTTGTGGTGCTCTGCAAAGAGGGCATTTTTCAGCTTTTCTTGCAATGGATTTGGAATGGACAATATGAGCTGTCGCCACTTCATAATTACCAACCAAAGCCAAAAGATCTGAGCCTGCCTTTTCTTTATTTCTTTAAATTGTTTTTCTTTCTTACTGCCTTTATCTATTTTAAGCAAAGTGGTCGGTTGAAACAATGGATAATTCACATTTAAATCATAAGAATCTTTTTCAAGTGTTCATTACATCCGTTTTGGTTCGTTTAAAATATTGTTTCCTATGCGCTCCTAGATGGGATACAGTACAAGTATTCAACTGTTGAGCAGAGATTTTTACCTCAAAAAATTAGT
+>TOG895871
+AGACACAACATCATAGAAACAGATCAACAACACATTAAAATTAGCATGGATCATAGCTTACGTTGTTTTGGGTCGACACTACCCAAAACTCTTCTTCAGTTTCTGTTATCACCTTCACTCCTTCTCTTCATCTCCTTCTTCAGTTTCTCCAACGCAGCCTTCGACCTCGCCACCATACCCTTCAACGATGCCTATTCACCCCTCTTTGGGGATGGCAACCTTGTCCGCTCCGCCGATGGCAACGGTGTTCAACTCCTCCTCGATCGCTTCACCGGTTCTGGTTTCGTTTCTTCCAATATGTACCAGCATGGATTCTTCAGCGCCAATATCAAGCTACCATCGAATTACAGCGCTGGTATTTGCGTGGCCTTTTATACATCAAACAATGAGATGTTTGAGAAGACACACGATGAGTTAGACTTTGAATTCTTAGGTAATATAGCCGGAAAGCCTTGGAGGTTTCAGACAAACTTGTACGGCAATGGCAGCACCAACCGTGGCCGTGAGGAGCGGTACCGCCTCTGGTTTGATCCAACCAAGGGATTCCATAGATACAGCATTCTATGGACAGCTAAGAACATCATATTTTACATAGATGAGGTTCCAATTAGAGAAATTATAAGAAGTGAAGAAATGGGAGCTGATTACCCAGCAAAGCCAATGGCATTATACGCCACAATATGGGATGCATCAAATTGGGCCACATCGGGTGGAAA
+>ADA84676.1 protein L-isoaspartyl methyltransferase 1 [Cicer arietinum]
+MEQYWSGSAINENKGMVENLQRYGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQPGMHALDVGSGTGYLTACFAMMVGPNGRAVGVEHIPELVSFSINNIEKSAAAPQLKDGSLSVHEGDGRQGWPEFATYDAIHVGAAAPEIPQPLIDQLKTGGRMIIPVGNVFQDLKVVDKNSDGSISIRTETSVRYVPLTSKEAQLKE
+>ADA84676.2 protein L-isoaspartyl methyltransferase 1 [Cicer arietinum]
+MEQYWSGSAGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQINENKGMVENLQRYPGMHALDVGSGTGYLTACFAMMVGPNGRAVGVEHIPELVSFSINNIEKSAAAPQLKDGSLSVHEGDGRQGWPEFATYDAIHVGAAAPEIPGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQPLIDQLKTGGRMIIPVGNVFQDLKVVDKNSDGSISIRTETGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQSVRYVPLTSKEAQLKE