quorum 0.1.0

data/lib/generators/templates/search

@@ -0,0 +1,141 @@
+#!/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
+