Class: Bio::Abif

Inherits:
SangerChromatogram show all
Defined in:
lib/bio/db/sanger_chromatogram/abif.rb

Overview

Description

This class inherits from the SangerChromatogram superclass. It captures the information contained within an ABIF format chromatogram file generated by DNA sequencing. See the SangerChromatogram class for usage.

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)

Attributes inherited from SangerChromatogram

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

Instance Method Summary (collapse)

Methods inherited from SangerChromatogram

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

Constructor Details

- (Abif) initialize(string)

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



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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

Instance Attribute Details

- (Object) chemistry

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



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

def chemistry
  @chemistry
end

- (Object) sample_title

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



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

def sample_title
  @sample_title
end

Instance Method Details

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

Returns the data for the name. If not found, returns nil.


Arguments:

  • (required) name: (String) name of the data

  • (required) tag_number: (Integer) tag number (default 1)

Returns

any data type or nil



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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