Module: Bio::Ngs::Illumina

Defined in:
lib/bio/ngs/illumina/fastq.rb,
lib/bio/ngs/illumina/sample.rb,
lib/bio/ngs/illumina/project.rb,
lib/bio/ngs/illumina/illumina.rb

Defined Under Namespace

Modules: FastqGz Classes: MetaReads, Project, Projects, Sample

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.build(path = ".") ⇒ Object 



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# File 'lib/bio/ngs/illumina/illumina.rb', line 38

def build(path=".")

  projects = Projects.new("Illumina", path)

  Dir.chdir(path) do
    Dir.glob(["**/Project_*","**/Undetermined_indices"]).each do |project_dir|
      project = Project.new(project_dir.sub(/.*Project_/,""),project_dir)
      projects.add(project)
      Dir.chdir(project_dir) do
        Dir.glob("Sample*").each do |sample_dir|
          sample = Sample.new(sample_dir.sub(/Sample_/,""), sample_dir, project)
          project.add(sample)
          Dir.chdir(sample_dir) do
            Dir.glob(["**/*.fastq", "**/*.fastq.gz"]) do |reads_filename|
              sample.add_filename(reads_filename)
            end
          end
        end
      end
    end
  end
  projects
end

.project_directory?(path = ".") ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/ngs/illumina/illumina.rb', line 21

def project_directory?(path=".")
  Dir.chdir(path) do
    projects = Dir.glob(["Project_*","Undetermined_indices"])
    return false if projects.empty?
    into_projects = projects.map do |project|
      Dir.chdir(project) do |sample|
        Dir.glob("Sample*").size>0
      end
    end.uniq

    if (into_projects.size>1 || (into_projects.first==false))
      return false
    end
  end
  true
end

Instance Method Details

#filter(file) ⇒ Object 



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# File 'lib/bio/ngs/illumina/fastq.rb', line 9

def filter(file)
  if File.exists? file
    filtered_file_basename = File.basename(file)
    filtered_dir =  File.join(File.dirname,"filtered")
    Dir.mkdir(filtered_dir) unless Dir.exists?(filtered_dir)
    FastqGz.gets_compressed(filtered_file_basename) do |compress|
      FastqGz.gets_filtered(ftest) do |read_header, reader_seq, read_splitter, read_qual|
       compress.write(read_header + reader_seq + read_splitter + read_qual)
      end
    end
 else
  raise "Bio::Ngs::Illumina.filter : unkown file #{file}"
 end 
end