quorum 0.5.2 → 0.6.0

data/spec/dummy/db/schema.rb

@@ -1,213 +0,0 @@
-# encoding: UTF-8
-# This file is auto-generated from the current state of the database. Instead
-# of editing this file, please use the migrations feature of Active Record to
-# incrementally modify your database, and then regenerate this schema definition.
-#
-# Note that this schema.rb definition is the authoritative source for your
-# database schema. If you need to create the application database on another
-# system, you should be using db:schema:load, not running all the migrations
-# from scratch. The latter is a flawed and unsustainable approach (the more migrations
-# you'll amass, the slower it'll run and the greater likelihood for issues).
-#
-# It's strongly recommended to check this file into your version control system.
-
-ActiveRecord::Schema.define(:version => 20120910180642) do
-
-  create_table "quorum_blastn_job_reports", :force => true do |t|
-    t.string   "query"
-    t.integer  "query_len"
-    t.string   "hit_id"
-    t.string   "hit_def"
-    t.string   "hit_accession"
-    t.integer  "hit_len"
-    t.integer  "hsp_num"
-    t.text     "hsp_group"
-    t.integer  "bit_score"
-    t.integer  "score"
-    t.string   "evalue"
-    t.integer  "query_from"
-    t.integer  "query_to"
-    t.integer  "hit_from"
-    t.integer  "hit_to"
-    t.string   "query_frame"
-    t.string   "hit_frame"
-    t.integer  "identity"
-    t.integer  "positive"
-    t.integer  "align_len"
-    t.text     "qseq"
-    t.text     "hseq"
-    t.text     "midline"
-    t.boolean  "results"
-    t.integer  "blastn_job_id"
-    t.datetime "created_at",     :null => false
-    t.datetime "updated_at",     :null => false
-    t.string   "hit_display_id"
-    t.integer  "gaps"
-  end
-
-  create_table "quorum_blastn_jobs", :force => true do |t|
-    t.string   "expectation"
-    t.integer  "max_score"
-    t.integer  "min_bit_score"
-    t.boolean  "filter"
-    t.boolean  "gapped_alignments"
-    t.integer  "gap_opening_penalty"
-    t.integer  "gap_extension_penalty"
-    t.text     "blast_dbs"
-    t.boolean  "queue"
-    t.integer  "job_id"
-    t.datetime "created_at",            :null => false
-    t.datetime "updated_at",            :null => false
-  end
-
-  create_table "quorum_blastp_job_reports", :force => true do |t|
-    t.string   "query"
-    t.integer  "query_len"
-    t.string   "hit_id"
-    t.string   "hit_def"
-    t.string   "hit_accession"
-    t.integer  "hit_len"
-    t.integer  "hsp_num"
-    t.text     "hsp_group"
-    t.integer  "bit_score"
-    t.integer  "score"
-    t.string   "evalue"
-    t.integer  "query_from"
-    t.integer  "query_to"
-    t.integer  "hit_from"
-    t.integer  "hit_to"
-    t.string   "query_frame"
-    t.string   "hit_frame"
-    t.integer  "identity"
-    t.integer  "positive"
-    t.integer  "align_len"
-    t.text     "qseq"
-    t.text     "hseq"
-    t.text     "midline"
-    t.boolean  "results"
-    t.integer  "blastp_job_id"
-    t.datetime "created_at",     :null => false
-    t.datetime "updated_at",     :null => false
-    t.string   "hit_display_id"
-    t.integer  "gaps"
-  end
-
-  create_table "quorum_blastp_jobs", :force => true do |t|
-    t.string   "expectation"
-    t.integer  "max_score"
-    t.integer  "min_bit_score"
-    t.boolean  "filter"
-    t.boolean  "gapped_alignments"
-    t.integer  "gap_opening_penalty"
-    t.integer  "gap_extension_penalty"
-    t.text     "blast_dbs"
-    t.boolean  "queue"
-    t.integer  "job_id"
-    t.datetime "created_at",            :null => false
-    t.datetime "updated_at",            :null => false
-  end
-
-  create_table "quorum_blastx_job_reports", :force => true do |t|
-    t.string   "query"
-    t.integer  "query_len"
-    t.string   "hit_id"
-    t.string   "hit_def"
-    t.string   "hit_accession"
-    t.integer  "hit_len"
-    t.integer  "hsp_num"
-    t.text     "hsp_group"
-    t.integer  "bit_score"
-    t.integer  "score"
-    t.string   "evalue"
-    t.integer  "query_from"
-    t.integer  "query_to"
-    t.integer  "hit_from"
-    t.integer  "hit_to"
-    t.string   "query_frame"
-    t.string   "hit_frame"
-    t.integer  "identity"
-    t.integer  "positive"
-    t.integer  "align_len"
-    t.text     "qseq"
-    t.text     "hseq"
-    t.text     "midline"
-    t.boolean  "results"
-    t.integer  "blastx_job_id"
-    t.datetime "created_at",     :null => false
-    t.datetime "updated_at",     :null => false
-    t.string   "hit_display_id"
-    t.integer  "gaps"
-  end
-
-  create_table "quorum_blastx_jobs", :force => true do |t|
-    t.string   "expectation"
-    t.integer  "max_score"
-    t.integer  "min_bit_score"
-    t.boolean  "filter"
-    t.boolean  "gapped_alignments"
-    t.integer  "gap_opening_penalty"
-    t.integer  "gap_extension_penalty"
-    t.text     "blast_dbs"
-    t.boolean  "queue"
-    t.integer  "job_id"
-    t.datetime "created_at",            :null => false
-    t.datetime "updated_at",            :null => false
-  end
-
-  create_table "quorum_jobs", :force => true do |t|
-    t.text     "sequence",      :null => false
-    t.text     "na_sequence"
-    t.text     "aa_sequence"
-    t.string   "sequence_hash"
-    t.datetime "created_at",    :null => false
-    t.datetime "updated_at",    :null => false
-  end
-
-  create_table "quorum_tblastn_job_reports", :force => true do |t|
-    t.string   "query"
-    t.integer  "query_len"
-    t.string   "hit_id"
-    t.string   "hit_def"
-    t.string   "hit_accession"
-    t.integer  "hit_len"
-    t.integer  "hsp_num"
-    t.text     "hsp_group"
-    t.integer  "bit_score"
-    t.integer  "score"
-    t.string   "evalue"
-    t.integer  "query_from"
-    t.integer  "query_to"
-    t.integer  "hit_from"
-    t.integer  "hit_to"
-    t.string   "query_frame"
-    t.string   "hit_frame"
-    t.integer  "identity"
-    t.integer  "positive"
-    t.integer  "align_len"
-    t.text     "qseq"
-    t.text     "hseq"
-    t.text     "midline"
-    t.boolean  "results"
-    t.integer  "tblastn_job_id"
-    t.datetime "created_at",     :null => false
-    t.datetime "updated_at",     :null => false
-    t.string   "hit_display_id"
-    t.integer  "gaps"
-  end
-
-  create_table "quorum_tblastn_jobs", :force => true do |t|
-    t.string   "expectation"
-    t.integer  "max_score"
-    t.integer  "min_bit_score"
-    t.boolean  "filter"
-    t.boolean  "gapped_alignments"
-    t.integer  "gap_opening_penalty"
-    t.integer  "gap_extension_penalty"
-    t.text     "blast_dbs"
-    t.boolean  "queue"
-    t.integer  "job_id"
-    t.datetime "created_at",            :null => false
-    t.datetime "updated_at",            :null => false
-  end
-
-end

data/spec/dummy/quorum/bin/fetch

@@ -1,115 +0,0 @@
-#!/usr/bin/env ruby
-
-$LOAD_PATH.unshift(File.expand_path("../../lib", __FILE__))
-
-require 'trollop'
-require 'fetch_tools/blast_db'
-
-FETCH_TOOLS = {
-  "blastdbcmd" => ["blastdbcmd"]
-}
-
-module Quorum
-  #
-  # Parse Options for Quorum Fetch
-  #
-  class Fetch
-
-    def initialize
-      opts = Trollop::options do
-        text <<-HEAD
-
-Quorum
-
-A flexible bioinformatics search tool.
-
-Options:
-
-        HEAD
-
-        # Fetch tool
-        opt :fetch_tool, "Fetch tool to execute. Available tools: " <<
-        "#{FETCH_TOOLS.keys.join(', ')}", :type => :string,
-          :required => true, :short => "-f"
-
-        # General settings
-        opt :log_directory, "Path to log directory", :type => :string,
-          :required => true, :short => "-l"
-        opt :tmp_directory, "Path to tmp directory", :type => :string,
-          :required => true, :short => "-m"
-
-        # Global settings
-        opt :fetch_database, "Path to fetch tool database", :type => :string,
-          :short => "-d"
-        opt :fetch_database_names, "Semicolon delimited database names",
-          :type => :string, :short => "-n"
-
-        # Algorithm specific opts
-        opt :blast_hit_id, "Blast hit id", :type => :string, :short => "-b"
-        opt :blast_hit_display_id, "Blast hit display id", :type => :string,
-          :short => "-s"
-        opt :blast_algo, "Blast algorithm", :type => :string, :short => "-a"
-      end
-
-      @args = {} # Contains valid opts.
-
-      ## Additional opt validation. ##
-
-      unless FETCH_TOOLS.keys.include?(opts[:fetch_tool].downcase)
-        Trollop::die :fetch_tool, "fetch_tool not found\n" <<
-        "Available tools: " + FETCH_TOOLS.keys.join(", ")
-      end
-
-      @args[:fetch_tool] = opts[:fetch_tool].downcase
-
-      unless opts[:fetch_database] && Dir.exists?(opts[:fetch_database])
-        Trollop::die :fetch_database, "fetch tool database not found\n" <<
-        "Supplied directory: " + opts[:fetch_database]
-      end
-
-      @args[:fetch_database]       = opts[:fetch_database]
-      @args[:fetch_database_names] = opts[:fetch_database_names]
-
-      unless Dir.exists?(opts[:log_directory])
-        Trollop::die :log_directory, "log directory not found\n" <<
-        "Supplied directory: " + opts[:log_directory]
-      end
-
-      @args[:log_directory]         = opts[:log_directory]
-      @args[:tmp_directory]         = opts[:tmp_directory]
-      @args[:blast_hit_id]          = opts[:blast_hit_id]
-      @args[:blast_hit_display_id]  = opts[:blast_hit_display_id]
-      @args[:blast_algo]            = opts[:blast_algo]
-
-      ## Check System Dependancies ##
-
-      check_dependencies
-
-      ## Execute fetch tool ##
-
-      if @args[:fetch_tool].include? "blastdbcmd"
-        blast = Quorum::FetchTools::BlastDb.new(@args)
-        blast.execute_blast_db_cmd
-      end
-    end
-
-    #
-    # Check system dependencies.
-    #
-    def check_dependencies
-      FETCH_TOOLS[@args[:fetch_tool]].each do |f|
-        system("which #{f} > /dev/null 2>&1")
-        if $?.exitstatus > 0
-          Trollop::die "Quorum dependency not found for tool " <<
-          "#{@args[:fetch_tool].to_s}. Please add `#{f}` to your PATH."
-        end
-      end
-    end
-
-  end
-end
-
-if __FILE__ == $0
-  Quorum::Fetch.new
-end
-

data/spec/dummy/quorum/bin/search

@@ -1,141 +0,0 @@
-#!/usr/bin/env ruby
-
-$LOAD_PATH.unshift(File.expand_path("../../lib", __FILE__))
-
-require 'trollop'
-require 'active_record'
-require 'search_tools/blast'
-
-# Quorum search tools and dependencies.
-SEARCH_TOOLS = {
-  "blastn"  => ["blastn"],
-  "blastx"  => ["blastx"],
-  "tblastn" => ["tblastn"],
-  "blastp"  => ["blastp"]
-}
-
-module Quorum
-  #
-  # Parse Options for Quorum Search Tools
-  #
-  class Search
-
-    def initialize
-      opts = Trollop::options do
-        text <<-HEAD
-
-Quorum
-
-A flexible bioinformatics search tool.
-
-Options:
-
-        HEAD
-
-        # Search tool
-        opt :search_tool, "Search tool to execute. Available tools: " <<
-        "#{SEARCH_TOOLS.keys.join(', ')}", :type => :string,
-          :required => true, :short => "-s"
-
-        # General settings
-        opt :log_directory, "Path to log directory", :type => :string,
-          :required => true, :short => "-l"
-        opt :tmp_directory, "Path to tmp directory", :type => :string,
-          :required => true, :short => "-m"
-
-        # ActiveRecord database settings
-        opt :id, "Database record ID", :type => :int, :required => true,
-          :short => "-i"
-        opt :database, "Database name", :type => :string, :required => true,
-          :short => "-d"
-        opt :database_adapter, "ActiveRecord database adapter",
-          :type => :string, :required => true, :short => "-a"
-        opt :database_host, "Database host", :type => :string,
-          :required => true, :short => "-k"
-        opt :database_user, "Database username", :type => :string,
-          :required => true, :short => "-u"
-        opt :database_password, "Database password", :type => :string,
-          :required => true, :short => "-p"
-
-        # Global settings
-        opt :search_database, "Path to search tool database", :type => :string,
-          :short => "-b"
-        opt :threads, "Number of threads to spawn for search tool",
-          :type => :int, :short => "-t"
-      end
-
-      @args = {} # Contains valid opts.
-
-      ## Additional opt validation. ##
-
-      unless SEARCH_TOOLS.keys.include?(opts[:search_tool].downcase)
-        Trollop::die :search_tool, "search_tool not found\n" <<
-        "Available search tools: " + SEARCH_TOOLS.keys.join(", ")
-      end
-
-      @args[:search_tool] = opts[:search_tool].downcase
-
-      unless opts[:search_database] && Dir.exists?(opts[:search_database])
-        Trollop::die :search_database, "search tool database not found\n" <<
-        "Supplied directory: " + opts[:search_database]
-      end
-
-      @args[:search_database] = opts[:search_database]
-
-      @args[:id]      = opts[:id]
-      @args[:threads] = opts[:threads]
-
-      unless Dir.exists?(opts[:log_directory])
-        Trollop::die :log_directory, "log directory not found\n" <<
-        "Supplied directory: " + opts[:log_directory]
-      end
-
-      @args[:log_directory] = opts[:log_directory]
-      @args[:tmp_directory] = opts[:tmp_directory]
-
-      ## Check System Dependancies ##
-
-      check_dependencies
-
-      ## Establish ActiveRecord Connection ##
-
-      begin
-        ActiveRecord::Base.establish_connection(
-          :adapter  => opts[:database_adapter],
-          :host     => opts[:database_host],
-          :username => opts[:database_user],
-          :password => opts[:database_password],
-          :database => opts[:database]
-        )
-      rescue Exception => e
-        Trollop::die puts e.message
-      end
-
-      ## Execute search tool ##
-
-      if @args[:search_tool].include? "blast"
-        blast = Quorum::SearchTools::Blast.new(@args)
-        blast.execute_blast
-      end
-    end
-
-    #
-    # Check system dependencies.
-    #
-    def check_dependencies
-      SEARCH_TOOLS[@args[:search_tool]].each do |b|
-        system("which #{b} > /dev/null 2>&1")
-        if $?.exitstatus > 0
-          Trollop::die "Quorum dependency not found for tool " <<
-          "#{@args[:search_tool].to_s}. Please add `#{b}` to your PATH."
-        end
-      end
-    end
-
-  end
-end
-
-if __FILE__ == $0
-  Quorum::Search.new
-end
-

data/spec/dummy/quorum/blastdb/test/contigs.fa

@@ -1,15 +0,0 @@
->TOG900080
-TGATAGGATAATTCTAGACAAAACATTAGCCGATCAAGTGTCATCATGGAAAAGCAGCAGGGGCCTTAGTGATACAGTGGTGACTGATCATGCTTGTTCTGGGGAAACATGCTCGTACTACGCAATTGGAGATGTATTTATTTGTGAAAAGACTGGACAAGTTCATGTTTGTGACGAAACATGTAGGGAAGTAGTAATGGATCCCACCAACGAGCTTTTGGTCTGTACAATATCTGGCCACTGTTTTGACAGATTGCTATCACCTGCTGAAATGGAGCCTGATGCTGAGCAGCAGCAAGGTGGTGCGGCAGATGAGGCAGAACCGTTTATGGGATCTGGCCGTTTTGCACGGGCTTATTTGCTGGGATACAATTGTGCTGATGAAAAGGAGCTTGAAGCTACTTTGAGGTTTTGCTGATCCCTATTGGCCCTTCTGGAGTGGATGATCTCATGTCTCAGCATTTACCTATTTAAGATCAAATAAATCGGGTTTCCTTTTCGTGTTTCTCTTGGCATAAGAATGTTTGATTAGATCTAGATTATGAAACTCTAATCGTCTTCTATATTAATAATTGTATGCTTAAATTTATAGTTGAAATTCCATTGATGAATTTTTCTT
->reverse translation of ADA84676.1 protein L-isoaspartyl methyltransferase 1 [Cicer arietinum] to a 687 base sequence of most likely codons.
-atggaacagtattggagcggcagcgcgattaacgaaaacaaaggcatggtggaaaacctg
-cagcgctatggcattattaaaagcagcaaagtggcggaaaccatggaaaaaattgatcgc
-ggcctgtttgtgccgaacggcgtgcagccgtatattgatagcccgatgagcattggctat
-aacgcgaccattagcgcgccgcatatgcatgcgacctgcctgcagctgctggaaaactat
-ctgcagccgggcatgcatgcgctggatgtgggcagcggcaccggctatctgaccgcgtgc
-tttgcgatgatggtgggcccgaacggccgcgcggtgggcgtggaacatattccggaactg
-gtgagctttagcattaacaacattgaaaaaagcgcggcggcgccgcagctgaaagatggc
-agcctgagcgtgcatgaaggcgatggccgccagggctggccggaatttgcgacctatgat
-gcgattcatgtgggcgcggcggcgccggaaattccgcagccgctgattgatcagctgaaa
-accggcggccgcatgattattccggtgggcaacgtgtttcaggatctgaaagtggtggat
-aaaaacagcgatggcagcattagcattcgcaccgaaaccagcgtgcgctatgtgccgctg
-accagcaaagaagcgcagctgaaagaa

data/spec/dummy/quorum/blastdb/test/peptides.fa

@@ -1,4 +0,0 @@
->ADA84676.1 protein L-isoaspartyl methyltransferase 1 [Cicer arietinum]
-MEQYWSGSAINENKGMVENLQRYGIIKSSKVAETMEKIDRGLFVPNGVQPYIDSPMSIGYNATISAPHMHATCLQLLENYLQPGMHALDVGSGTGYLTACFAMMVGPNGRAVGVEHIPELVSFSINNIEKSAAAPQLKDGSLSVHEGDGRQGWPEFATYDAIHVGAAAPEIPQPLIDQLKTGGRMIIPVGNVFQDLKVVDKNSDGSISIRTETSVRYVPLTSKEAQLKE
->VIRT10447
-TVLPHLPHHLAAAQHQAPFQQVIAICQNSGQILYRPKARWWDPLLLPYMFRHKHELVQSFHK

data/spec/dummy/quorum/blastdb/test.nhd

@@ -1,2 +0,0 @@
-34432766131
-8824380950

data/spec/dummy/quorum/blastdb/test.nsd

@@ -1,2 +0,0 @@
-gnl|bl_ord_id|00
-gnl|bl_ord_id|11

data/spec/dummy/quorum/blastdb/test.phd

@@ -1,2 +0,0 @@
-24330897691
-28413460680

data/spec/dummy/quorum/blastdb/test.psd

@@ -1,2 +0,0 @@
-gnl|bl_ord_id|00
-gnl|bl_ord_id|11

data/spec/dummy/quorum/lib/fetch_tools/blast_db.rb

@@ -1,106 +0,0 @@
-$LOAD_PATH.unshift(File.expand_path("../../", __FILE__))
-
-require 'logger'
-
-module Quorum
-  module FetchTools
-    #
-    # Blast DB Fetch Tool
-    #
-    class BlastDb
-
-      # blastdbcmd -dbtype
-      DB_TYPE = {
-        "blastn"  => "nucl",
-        "blastx"  => "prot",
-        "tblastn" => "nucl",
-        "blastp"  => "prot"
-      }
-
-      private
-
-      def initialize(args)
-        @tool           = args[:fetch_tool]
-        @entry          = args[:blast_hit_id]
-        @hit_display_id = args[:blast_hit_display_id]
-        @blast_algo     = args[:blast_algo]
-        @log_directory  = args[:log_directory]
-        @tmp_directory  = args[:tmp_directory]
-        @fetch_database = args[:fetch_database]
-        @databases      = args[:fetch_database_names]
-
-        @logger = Quorum::Logger.new(@log_directory)
-
-        @db = @databases.split(';')
-        @db.map! { |d| File.join(@fetch_database, d) }
-
-        @db_type = DB_TYPE[@blast_algo]
-        @db_type ||= 'guess'
-      end
-
-      #
-      # Generate the blastdbcmd(s).
-      #
-      def generate_blast_db_cmds
-        @cmds = []
-        @db.each do |d|
-          blastdbcmd = "blastdbcmd " <<
-          "-db '#{d}' " <<
-          "-dbtype '#{@db_type}' " <<
-          "-entry '#{@entry}' "
-          @cmds << blastdbcmd
-        end
-      end
-
-      #
-      # Parse the blastdbcmd returned sequence(s) and delete if @hit_display_id
-      # is not present.
-      #
-      def parse_and_send_results
-        seqs = @seqs.split('>')
-        seqs.delete_if { |s| s.empty? || !s.include?(@hit_display_id) }
-        if seqs.length != 1
-          @logger.log(
-            "Quorum::FetchTools::BlastDb#parse_and_send_results",
-            "blastdbcmd returned #{seqs.length} sequence(s). Please ensure " <<
-            "your Blast database source FASTA headers are unique across ALL " <<
-            "databases. See the entry above for details."
-          )
-          "An error occurred while processing your request."
-        else
-          ">" << seqs.first
-        end
-      end
-
-      public
-
-      #
-      # Execute the blastdbcmd(s) and return the matching sequence.
-      #
-      # To make Blast execute as quickly as possible, each selected
-      # algorithm blasts against all supplied databases at once.
-      #
-      # See quorum/lib/search_tools/blast.rb for more information.
-      #
-      # One consequence of this is not knowing which Blast database to use
-      # when retrieving a hit sequence via blastdbcmd.
-      #
-      # See blastdbcmd -help for more information.
-      #
-      # To work around this issue, simply execute blastdbcmd against all
-      # Blast databases and filter on hit_display_id.
-      #
-      def execute_blast_db_cmd
-        generate_blast_db_cmds
-        @logger.log("NCBI Blast", @cmds.join('; '))
-
-        @seqs = ""
-        @cmds.each { |c| @seqs << `#{c} 2> /dev/null` }
-
-        seq = parse_and_send_results
-        $stdout.print seq
-      end
-
-    end
-  end
-end

data/spec/dummy/quorum/lib/logger.rb

@@ -1,43 +0,0 @@
-module Quorum
-  class Logger
-
-    def initialize(dir)
-      @log_directory = dir
-      @log_file      = "quorum.log"
-    end
-
-    #
-    # Write to log file and exit if exit_status is present.
-    #
-    def log(program, message, exit_status = nil, files = nil)
-      File.open(File.join(@log_directory, @log_file), "a") do |log|
-        log.puts ""
-        log.puts Time.now.to_s + " " + program
-        log.puts message
-        log.puts ""
-      end
-
-      if exit_status
-        remove_files(files) unless files.nil?
-        exit exit_status.to_i
-      end
-    end
-
-    private
-
-    #
-    # Removes instance files.
-    #
-    def remove_files(files)
-      if Dir.glob(files).empty?
-         log(
-          "remove_files",
-          "Unable to remove #{files}"
-        )
-      else
-       `rm #{files}`
-      end
-    end
-
-  end
-end