Class: AssemblyPipe::VelvetOptimiser::LogFile

Inherits:
Object
  • Object
show all
Defined in:
lib/assembly_pipe.rb,
bin/assembly_pipe

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(filename) ⇒ LogFile

Returns a new instance of LogFile.



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# File 'lib/assembly_pipe.rb', line 27

def initialize(filename)
  @lines = File.readlines(filename).map{|line| line.strip}
end

Class Method Details

.open(filename) ⇒ Object 



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# File 'lib/assembly_pipe.rb', line 31

def self.open(filename)
  self.new(filename)
end

Instance Method Details

#date ⇒ Object 



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# File 'lib/assembly_pipe.rb', line 35

def date
  Time.parse(@lines.first)
end

#final_assembly ⇒ Object 



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# File 'lib/assembly_pipe.rb', line 100

def final_assembly
  run = {}
  @lines.drop_until{|line| line.match(/Final optimised assembly details/)}.
    take_while{|line| !line.match(/Assembly output files are in the following directory/)}.
    each do |line|
    key, value = line.split(":",2)
    case key
    when /Assembly id/,
      /Assembly score/,
      /Roadmap file size/,
      /Total number of contigs/,
      /n50/,
      /length of longest contig/,
      /Total bases in contigs/,
      /Number of contigs/,
      /Total bases in contigs/
      run[key] = value.to_i
    when /timestamp/
      run[key] = Time.parse(value)
    when /version/,
      /Readfile/,
      /parameter string/,
      /Velvet hash value/,
      /Paired Library insert stats/
      run[key] = value.strip
    end
  end
  run
end

#summary_table ⇒ Object 



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# File 'lib/assembly_pipe.rb', line 130

def summary_table
  vvgs = vanilla_velvetg_runs.map{|run| run["Run class"] = "vanilla"; run}
  final = final_assembly
  final["Run class"] = "optimised"

  all_keys = vvgs.map{|run| run.keys}.flatten + final_assembly.keys
  all_keys.uniq!
  output = ''
  output << all_keys.join("\t") + "\n"
  vvgs.each do |run|
    output << all_keys.map{|key| run[key] }.join("\t") + "\n"
  end
  output << all_keys.map{|key| final[key] }.join("\t") + "\n"
end

#vanilla_velvetg_runs ⇒ Object 



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# File 'lib/assembly_pipe.rb', line 66

def vanilla_velvetg_runs
  Enumerator.new do |yielder|
    run = {}
    @lines.drop_until{|line| line.match(/Beginning vanilla velvetg runs/)}.
      take_while{|line| !line.match(/Best assembly by assembly score/)}.
      each do |line|
      key,value = line.split(":",2)
      case key
      when /Assembly id/,
        /Assembly score/,
        /Velvet hash value/,
        /Roadmap file size/,
        /Total number of contigs/,
        /n50/,
        /length of longest contig/,
        /Total bases in contigs/,
        /Number of contigs/,
        /Total bases in contigs/            
        run[key] = value.to_i
      when /timestamp/
        run[key] = Time.parse(value)
      when /version/,
        /Readfile/,
        /parameter string/,
        /Assembly directory/
        run[key] = value.strip
      when /\*{10,}/
        yielder << run unless run.keys.empty?
        run = {}
      end
    end
  end
end

#velveth_runs ⇒ Object 



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# File 'lib/assembly_pipe.rb', line 39

def velveth_runs
  Enumerator.new do |yielder|
    run = {}
    @lines.drop_until{|line| line.match(/Beginning velveth runs/)}.
      take_while{|line| !line.match(/Beginning vanilla velvetg runs/)}.
      each do |line|
      key, value = line.split(":",2)
      case key
      when /Velveth version/,
        /Readfile/,
        /Velveth parameter string/,
        /Assembly directory/
        run[key] = value.strip
      when /Velveth timestamp/
        run[key] = Time.parse(value)
      when /Assembly id/,
        /Velvet hash value/,
        /Roadmap file size/
        run[key] = value.to_i
      when /\*{10,}/
        yielder << run unless run.keys.empty?
        run = {}
      end
    end
  end
end