Class: Bio::Abif

Inherits:

SangerChromatogram

• Object
• SangerChromatogram
• Bio::Abif

show all

Defined in:

lib/bio/db/sanger_chromatogram/abif.rb

Overview

Defined Under Namespace

Classes: DirectoryEntry

Constant Summary

DATA_TYPES =

{ 1 => 'byte', 2 => 'char', 3 => 'word', 4 => 'short', 5 => 'long',
7 => 'float', 8 => 'double', 10 => 'date', 11 => 'time', 18 => 'pString',
19 => 'cString', 12 => 'thumb', 13 => 'bool', 6 => 'rational', 9 => 'BCD',
14 => 'point', 15 => 'rect', 16 => 'vPoint', 17 => 'vRect', 20 => 'tag',
128 => 'deltaComp', 256 => 'LZWComp', 384 => 'deltaLZW', 1024 => 'user'}

PACK_TYPES =

User defined data types have tags numbers >= 1024

{ 'byte' => 'C', 'char' => 'c', 'word' => 'n', 'short' => 'n', 'long' => 'N',
'date' => 'nCC', 'time' => 'CCCC', 'pString' => 'CA*', 'cString' => 'Z*',
'float' => 'g', 'double' => 'G',
'bool' => 'C', 'thumb' => 'NNCC', 'rational' => 'NN', 'point' => 'nn', 
'rect' => 'nnnn', 'vPoint' => 'NN', 'vRect' => 'NNNN', 'tag' => 'NN'}

Instance Attribute Summary (collapse)

• - (Object) chemistry

  The chemistry used when sequencing e.g Dye terminators => 'term.' (String).

• - (Object) sample_title

  The sample title as entered when sequencing the sample (String).

Attributes inherited from SangerChromatogram

#atrace, #chromatogram_type, #ctrace, #dye_mobility, #gtrace, #peak_indices, #qualities, #sequence, #ttrace, #version

Instance Method Summary (collapse)

• - (Object) data(name, tag_number = 1)

  Returns the data for the name.

• - (Abif) initialize(string) constructor

  see SangerChromatogram class for how to create an Abif object and its usage.

Methods inherited from SangerChromatogram

#complement, #complement!, open, #seq, #sequence_string, #to_biosequence

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# File 'lib/bio/db/sanger_chromatogram/abif.rb', line 37

def initialize(string)
  header = string.slice(0,128)
  # read in header info
  @chromatogram_type, @version, @directory_tag_name, @directory_tag_number, @directory_element_type, @directory_element_size, @directory_number_of_elements, @directory_data_size, @directory_data_offset, @directory_data_handle= header.unpack("a4 n a4 N n n N N N N")
  @version = @version/100.to_f
  get_directory_entries(string)
  # get sequence
  @sequence = @directory_entries["PBAS"][1].data.map{|char| char.chr.downcase}.join("")
  #get peak indices
  @peak_indices = @directory_entries["PLOC"][1].data
  #get qualities
  @qualities = @directory_entries["PCON"][1].data
  # get sample title
  @sample_title = @directory_entries["SMPL"][1].data
  @directory_entries["PDMF"].size > 2 ? @dye_mobility = @directory_entries["PDMF"][2].data : @dye_mobility = @directory_entries["PDMF"][1].data
  #get trace data
  @chemistry = @directory_entries["phCH"][1].data
  base_order = @directory_entries["FWO_"][1].data.map{|char| char.chr.downcase}
  (9..12).each do |data_index|
    self.instance_variable_set("@#{base_order[data_index-9]}trace", @directory_entries["DATA"][data_index].data)
  end

end

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# File 'lib/bio/db/sanger_chromatogram/abif.rb', line 34

def chemistry
  @chemistry
end

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# File 'lib/bio/db/sanger_chromatogram/abif.rb', line 32

def sample_title
  @sample_title
end

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# File 'lib/bio/db/sanger_chromatogram/abif.rb', line 68

def data(name, tag_number = 1)
  d = @directory_entries[name]
  d ? d[tag_number].data : nil
end