#!/usr/bin/env ruby

#
# run crb-blast from the cli
#

require 'trollop'
require 'crb-blast'
require 'bindeps'

opts = Trollop::options do
  version CRB_Blast::VERSION::STRING.dup
  banner <<-EOS

CRB-Blast v#{CRB_Blast::VERSION::STRING.dup} by Chris Boursnell <cmb211@cam.ac.uk>

Conditional Reciprocal Best BLAST

USAGE:
crb-blast <options>

OPTIONS:

EOS
  opt :query,
      "query fasta file",
      :required => true,
      :type => String

  opt :target,
      "target fasta file",
      :required => true,
      :type => String

  opt :evalue,
      "e-value cut off for BLAST. Format 1e-5",
      :default => 1e-5,
      :type => :float

  opt :threads,
      "number of threads to run BLAST with",
      :default => 1,
      :type => :int

  opt :output,
      "output file as tsv",
      :required => true,
      :type => String

  opt :split,
      "split the fasta files into chunks and run multiple blast jobs and then"+
      " combine them."
end

Trollop::die :query, "must exist" if !File.exist?(opts[:query])
Trollop::die :target, "must exist" if !File.exist?(opts[:target])

gem_dir = Gem.loaded_specs['crb-blast'].full_gem_path
gem_deps = File.join(gem_dir, 'deps', 'deps.yaml')
Bindeps.require gem_deps

blaster = CRB_Blast::CRB_Blast.new(opts.query, opts.target)
dbs = blaster.makedb
run = blaster.run_blast(opts.evalue, opts.threads, opts.split)
load = blaster.load_outputs
recips = blaster.find_reciprocals
secondaries = blaster.find_secondaries

File.open("#{opts.output}", 'w') do |out|
  blaster.reciprocals.each_pair do |query_id, hits|
    hits.each do |hit|
      out.write "#{hit}\n"
    end
  end
end