Class: Bio::Ngs::Illumina::Sample

Inherits:
Meta::Pool show all
Defined in:
lib/bio/ngs/illumina/sample.rb

Overview

File

Instance Attribute Summary

Attributes inherited from Meta::Pool

#pool

Attributes inherited from Meta::Data

#metadata

Instance Method Summary collapse

Methods inherited from Meta::Pool

#add, #each, #empty?, #get, #get_by_name, #get_by_tag, #get_by_tag_and_value, #get_by_value, #get_down_to_childer, json_create, #names

Methods included from Enumerable

#average, #sample_variance, #standard_deviation, #sum

Methods inherited from Meta::Data

#==, #[], #has_tag?, #has_value?, json_create, #name, #name=

Constructor Details

#initialize(name, path, parent = nil) ⇒ Sample

attr_accessor :name #, :filenames



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# File 'lib/bio/ngs/illumina/sample.rb', line 31

def initialize(name, path, parent=nil)
  super(name)
  metadata[:path]=path
  @parent = parent
end

Instance Method Details

#add_filename(filename) ⇒ Object 



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# File 'lib/bio/ngs/illumina/sample.rb', line 45

def add_filename(filename)
filename_metadata = filename.dup
metadata = {:filename=>filename_metadata}
#TODO maybe could be usefult to leave this to end used, define what is a filtered/trimmed file. Define a regexp for each category.
if filename=~/trimmed|TRIMMED/
  metadata[:trimmed] = true
  metadata[:trimmed_aggregated] = true unless filename=~/_\d+\./
end

if filename=~/filtered|FILTERED/
  metadata[:filtered] = true
  metadata[:filtered_aggregated] =true unless filename=~/_\d+\./
end
metadata[:left] = true if filename=~/.*_R1_.*/
metadata[:right] = true if filename=~/.*_R2_.*/
metadata[:zipped] = true if filename=~/\.gz/
metadata[:aggregated] = true unless metadata[:trimmed_aggregated] || metadata[:filtered_aggregated] || filename=~/_\d+\./

filename.sub!(/_([ACGT]+)_/,'_')
metadata[:index] = $1
filename.sub!(/_L([0-9]+)_?/,'_')
metadata[:lane] = $1

#filename_cleaned = filename.sub(/_R.*/,'')
readsdata_name = File.basename(filename).sub(/TRIMMED/,'').sub(/trimmed/,'').sub(/filtered/,'').sub(/FILTERED/,'').sub(/_R\d+_\d+_?/,'').sub(/_R\d+_/,'').sub(/\..+$/,'') #TODO is not the best thing to do

  if filename=~/R._(\d*).fastq(.gz)?/
    metadata[:chunks]=$1
  end
  self.add MetaReads.new(SecureRandom.uuid, metadata)
end

#filenames_paths ⇒ Object

REMOVE # def get(tag=filtered)

@files.get(tag)

end



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# File 'lib/bio/ngs/illumina/sample.rb', line 81

def filenames_paths
  @filenames.keys.map do |filename|
    filename_path(filename)
  end.flatten
end

#paired? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/ngs/illumina/sample.rb', line 41

def paired?
  @filenames.key?(:left) && @filenames.key?(:right)
end

#path ⇒ Object 



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# File 'lib/bio/ngs/illumina/sample.rb', line 37

def path
  File.join @parent.path,"Sample_#{name}"
end

#to_json(*a) ⇒ Object 



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# File 'lib/bio/ngs/illumina/sample.rb', line 87

def to_json(*a)
  {
    "json_class"   => self.class.name,
    "name"         => name,
    "metadata"     => metadata,
    "files"        => pool
  }.to_json(*a)
end