MGBparser.rb

#!/usr/bin/env ruby

class MultiGeneBlast
  attr :file, :query, :genes, :hits

  def initialize(file)
    @file = file
    @genes = MultiGeneBlast::Set.new
    @hits  = MultiGeneBlast::Set.new
    load_from_file!
  end

  def load_from_file!
    File.open(file, "r") do |fh|
      load_header(fh)
      load_hits(fh)
      load_details(fh)
    end
  end

  private
    def load_header(fh)
      while !fh.eof?
        ln = fh.gets.chomp
        case ln
        when '', /\ATable of genes, .*:/ # Do nothing
        when /\ASignificant hits:/ ; break
        when /\AClusterBlast scores for (.*)/
          @query = $1
        else
          @genes << MultiGeneBlast::Gene.new(ln)
        end
      end
    end
    def load_hits(fh)
      while !fh.eof?
        case fh.gets.chomp
        when '' # Do nothing
        when /\ADetails:/ ; break
        when /\A(\d+)\. (\S+)\s+(.*)\./
          @hits << MultiGeneBlast::Hit.new($1, $2, $3)
        end
      end
    end
    def load_details(fh)
      while !fh.eof?
        hit = load_details_header(fh)
        load_details_genes(fh, hit)
        load_details_hits(fh, hit)
      end
    end
    def load_details_header(fh)
      h = nil
      while !fh.eof?
        case fh.gets.chomp
        when '', '>>' # Do nothing
        when /\ATable of genes, .*:/ ; break
        when /\A(\d+)\. (.*)/
          h = @hits[$1.to_i]
          raise "Bad name: got #{$2}, expected #{h.gene}" if h.gene!=$2
        when /\ASource: (.*)\./
          raise "Bad source: got #{$1}, expected #{h.source}" if h.source!=$1
        when /\ANumber .* hits to this cluster: (\d+)/
          h.proteins_with_hits = $1.to_i
        when /\AMultiGeneBlast score: ([\d\.]+)/
          h.score = $1.to_f
        when /\ACumulative Blast bit score: ([\d\.]+)/
          h.cumulative_score = $1.to_f
        end
      end
      h
    end
    def load_details_genes(fh, hit)
      while !fh.eof?
        ln = fh.gets.chomp
        case ln
        when '' # Do nothing
        when /\ATable of Blast hits .*:/ ; break
        else
          hit.genes << MultiGeneBlast::Gene.new(ln)
        end
      end
    end
    def load_details_hits(fh, hit)
      while !fh.eof?
        ln = fh.gets.chomp
        case ln
        when '' # Do nothing
        when '>>' ; break
        else
          hit.blast_hits << MultiGeneBlast::BlastHit.new(ln)
        end
      end
    end
end

class MultiGeneBlast::Gene
  attr :name, :loc_start, :loc_end, :strand, :annotation, :locus_tag
  alias index name
  
  def initialize(str)
    s = str.split(/\s+/)
    [1,2].each{ |i| s[i] = s[i].to_i }
    @name, @loc_start, @loc_end, @strand, @annotation, @locus_tag = *s
  end
end

class MultiGeneBlast::Hit
  attr :rank, :gene, :source
  attr_accessor :proteins_with_hits, :score, :cumulative_score
  attr_accessor :genes, :blast_hits
  alias index rank
  
  def initialize(rank, gene, source)
    @rank, @gene, @source = rank.to_i, gene, source
    @genes = MultiGeneBlast::Set.new
    @blast_hits = MultiGeneBlast::Set.new
  end
end

class MultiGeneBlast::BlastHit
  attr :query, :subject, :identity, :score, :coverage, :evalue
  alias index subject

  def initialize(str)
    s = str.split(/\s+/)
    (2..5).each{ |i| s[i] = s[i].to_f }
    @query, @subject, @identity, @score, @coverage, @evalue = *s
  end
end

class MultiGeneBlast::Set < Hash
  def <<(v) self[v.index]=v ; end
end

# Main:
file = ARGV.shift
unless file
  $stderr.puts "Usage: #{__FILE__} MultiGeneBlast.txt"
  exit 0
end

mgb = MultiGeneBlast.new(file)