Class: Cheripic::Regions

Inherits:
Object
  • Object
show all
Extended by:
Forwardable
Includes:
Enumerable
Defined in:
lib/cheripic/regions.rb

Overview

An application of Bio::DB::Fasta object that lets to extract selected regions of the fasta entries

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(assembly) ⇒ Regions

creates a Regions object using fasta

Parameters:

  • assembly (String) —

    path to a fasta file



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# File 'lib/cheripic/regions.rb', line 26

def initialize(assembly)
  @reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>assembly})
  @id_len = {}
  self.get_id_len
end

Instance Attribute Details

#id_len ⇒ Hash (readonly)

Returns a hash of fasta entry ids as keys and sequence length as values.

Returns:

  • (Hash) —

    a hash of fasta entry ids as keys and sequence length as values



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# File 'lib/cheripic/regions.rb', line 16

class Regions

  include Enumerable
  extend Forwardable
  def_delegators :@id_len, :each, :each_key, :each_value, :length, :[]
  attr_reader :reference_db, :id_len

  # creates a Regions object using fasta
  #
  # @param assembly [String] path to a fasta file
  def initialize(assembly)
    @reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>assembly})
    @id_len = {}
    self.get_id_len
  end

  # A method to extract fasta entry ids and length and make a hash
  #
  # @return [Hash] a hash of fasta entry ids as keys and sequence length as values
  def get_id_len
    @reference_db.load_fai_entries
    @reference_db.index.entries.each_entry do | entry |
      @id_len[entry.id] = entry.length
    end
  end

  # A method to returns left and right sequence of specified length, for a provided id and position
  # @note this method excludes the base at the position provided
  # @param id [String]
  # @param pos [Integer]
  # @return [Array<String>]
  def fetch_seq(id, pos)
    limit = Options.sel_seq_len + 1
    len = @id_len[id]
    low = pos-limit <= 0 ? 0 : pos-limit
    high = pos+limit >= len ? len : pos+limit
    region = Bio::DB::Fasta::Region.parse_region("#{id}:#{low}-#{pos-1}")
    seq_left = @reference_db.fetch_sequence(region)
    region = Bio::DB::Fasta::Region.parse_region("#{id}:#{pos+1}-#{high}")
    seq_right = @reference_db.fetch_sequence(region)
    [seq_left, seq_right]
  end

end

#reference_db ⇒ Bio::DB::Fasta::FastaFile (readonly)

Returns indexed fasta object.

Returns:

  • (Bio::DB::Fasta::FastaFile) —

    indexed fasta object



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# File 'lib/cheripic/regions.rb', line 16

class Regions

  include Enumerable
  extend Forwardable
  def_delegators :@id_len, :each, :each_key, :each_value, :length, :[]
  attr_reader :reference_db, :id_len

  # creates a Regions object using fasta
  #
  # @param assembly [String] path to a fasta file
  def initialize(assembly)
    @reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>assembly})
    @id_len = {}
    self.get_id_len
  end

  # A method to extract fasta entry ids and length and make a hash
  #
  # @return [Hash] a hash of fasta entry ids as keys and sequence length as values
  def get_id_len
    @reference_db.load_fai_entries
    @reference_db.index.entries.each_entry do | entry |
      @id_len[entry.id] = entry.length
    end
  end

  # A method to returns left and right sequence of specified length, for a provided id and position
  # @note this method excludes the base at the position provided
  # @param id [String]
  # @param pos [Integer]
  # @return [Array<String>]
  def fetch_seq(id, pos)
    limit = Options.sel_seq_len + 1
    len = @id_len[id]
    low = pos-limit <= 0 ? 0 : pos-limit
    high = pos+limit >= len ? len : pos+limit
    region = Bio::DB::Fasta::Region.parse_region("#{id}:#{low}-#{pos-1}")
    seq_left = @reference_db.fetch_sequence(region)
    region = Bio::DB::Fasta::Region.parse_region("#{id}:#{pos+1}-#{high}")
    seq_right = @reference_db.fetch_sequence(region)
    [seq_left, seq_right]
  end

end

Instance Method Details

#fetch_seq(id, pos) ⇒ Array<String>

Note:

this method excludes the base at the position provided

A method to returns left and right sequence of specified length, for a provided id and position

Parameters:

  • id (String)
  • pos (Integer)

Returns:

  • (Array<String>) 


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# File 'lib/cheripic/regions.rb', line 47

def fetch_seq(id, pos)
  limit = Options.sel_seq_len + 1
  len = @id_len[id]
  low = pos-limit <= 0 ? 0 : pos-limit
  high = pos+limit >= len ? len : pos+limit
  region = Bio::DB::Fasta::Region.parse_region("#{id}:#{low}-#{pos-1}")
  seq_left = @reference_db.fetch_sequence(region)
  region = Bio::DB::Fasta::Region.parse_region("#{id}:#{pos+1}-#{high}")
  seq_right = @reference_db.fetch_sequence(region)
  [seq_left, seq_right]
end

#get_id_len ⇒ Hash

A method to extract fasta entry ids and length and make a hash

Returns:

  • (Hash) —

    a hash of fasta entry ids as keys and sequence length as values



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# File 'lib/cheripic/regions.rb', line 35

def get_id_len
  @reference_db.load_fai_entries
  @reference_db.index.entries.each_entry do | entry |
    @id_len[entry.id] = entry.length
  end
end