#!/usr/bin/env ruby

require 'optparse'
require 'bio-logger'
require 'bio-velvet'
require 'pp'

SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = 'finishm'
$:.unshift File.join(File.dirname(__FILE__),'..','lib')
require 'priner'

# Parse command line options into the options hash
options = {
  :logger => 'stderr',
  :log_level => 'info',
}
global = OptionParser.new do |opts|
  opts.banner = "
    Usage: #{SCRIPT_NAME} <command> [<arguments>]

  FinishM is a collection of tasks related to assembly and metagenome assembly. Common commands:

    roundup\tImprove a genome by connecting scaffolds and gapfilling
    visualise\tVisualise the DeBruijn graph

  Other available commands:

    wander\tTry to connect contigs (experimental)
    gapfill\tFill assembly gaps (N characters) (experimental)
    explore\tWhat happens in the graph beyond the end of my contig(s)? (experimental)
"+ # primer stuff is not really ready and requires bio-primer3 to be released.
  # Commands for PCR finishing:

  #   primers\tdesign primers for multi-primer multi-lane PCR experimental setup (experimental)
  #   primers_check\ttest a set of primers for incompatibility (experimental)
  #   finish\tprocess results from multi-primer multi-lane PCR experimental setup (experimental)
"
  Utility modes:

    sequence\tGiven a defined sequence of nodes, what is the corresponding sequence?
    count_paths\tCount the number of paths through assembly graph
    find_orfs\tFind possible open reading frames in assembly graph
    \n\n"
end
global.order!

operator = nil
subcommands = {
  # 'primers' => lambda {OptionParser.new do |opts|
  #   operator = Bio::FinishM::Primers.new
  #   operator.add_options(opts, options)
  # end},
  # 'primers_check' => lambda {OptionParser.new do |opts|
  #   operator = Bio::FinishM::Primers::Checker.new
  #   operator.add_options(opts, options)
  # end},
  # 'finish' => lambda {OptionParser.new do |opts|
  #   operator = Bio::FinishM::Finisher.new
  #   operator.add_options(opts, options)
  # end},
  'gapfill' => lambda {OptionParser.new do |opts|
    operator = Bio::FinishM::GapFiller.new
    operator.add_options(opts, options)
  end},
  'wander' => lambda {OptionParser.new do |opts|
    operator = Bio::FinishM::Wanderer.new
    operator.add_options(opts, options)
  end},
  'fluff' => lambda {OptionParser.new do |opts|
    operator = Bio::FinishM::Fluff.new
    operator.add_options(opts, options)
  end},
  'explore' => lambda {OptionParser.new do |opts|
    operator = Bio::FinishM::Explorer.new
    operator.add_options(opts, options)
  end},
  'assemble' => lambda {OptionParser.new do |opts|
    operator = Bio::FinishM::Assembler.new
    operator.add_options(opts, options)
  end},
  'visualise' => lambda {OptionParser.new do |opts|
    operator = Bio::FinishM::Visualise.new
    operator.add_options(opts, options)
  end},
  'sequence' => lambda {OptionParser.new do |opts|
    operator = Bio::FinishM::Sequence.new
    operator.add_options(opts, options)
  end},
  'roundup' => lambda {OptionParser.new do |opts|
    operator = Bio::FinishM::RoundUp.new
    operator.add_options(opts, options)
  end},
  'count_paths' => lambda {OptionParser.new do |opts|
    operator = Bio::FinishM::PathCounter.new
    operator.add_options(opts, options)
  end},
  'find_orfs' => lambda {OptionParser.new do |opts|
    operator = Bio::FinishM::ORFsFinder.new
    operator.add_options(opts, options)
  end}
}

subcommand = nil
if ARGV[0] and ARGV[0].match(/finishm$/) #if debugging e.g. 'pry finishm wander ..'. But be careful of finishm no arguments
  subcommand = ARGV.shift
  subcommand = ARGV.shift
else
  # not debugging
  subcommand = ARGV.shift
end

if subcommand.nil?
  $stderr.puts global
  exit 1
elsif !subcommands[subcommand]
  $stderr.puts "Unrecognized subcommand: #{subcommand}"
  exit 1
else
  # Add options specific for subcommand
  opts = subcommands[subcommand].call

  # Add global logging options
  opts.separator "\nVerbosity:\n\n"
  opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {options[:log_level] = 'error'}
  opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
  opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| options[:log_level] = s}
  opts.separator "\n"
  opts.parse!

  # Setup logging
  Bio::Log::CLI.logger(options[:logger]); Bio::Log::CLI.trace(options[:log_level]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME); log.outputters.each {|o| o.formatter = Log4r::PatternFormatter.new(:pattern => "%5l %c %d: %m", :date_pattern => '%d/%m %T')}
  Bio::Log::LoggerPlus.new 'bio-velvet'; Bio::Log::CLI.configure 'bio-velvet'

  log.debug "Running FinishM #{subcommand} with these options: #{PP.pp(options, "").gsub(/\n$/,'')}"

  error_message = operator.validate_options(options, ARGV)
  if error_message.nil? or error_message == false
    operator.run options, ARGV
  else
    $stderr.puts
    $stderr.puts "ERROR parsing options: #{error_message}"
    $stderr.puts
    $stderr.puts opts
    exit 1
  end
end