class Bio::Abif

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.

Constants

DATA_TYPES
PACK_TYPES

Attributes

chemistry[RW]

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

sample_title[RW]

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

Public Class Methods

new(string) click to toggle source

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

   # File lib/bio/db/sanger_chromatogram/abif.rb
37 def initialize(string)
38   header = string.slice(0,128)
39   # read in header info
40   @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")
41   @version = @version/100.to_f
42   get_directory_entries(string)
43   # get sequence
44   @sequence = @directory_entries["PBAS"][1].data.map{|char| char.chr.downcase}.join("")
45   #get peak indices
46   @peak_indices = @directory_entries["PLOC"][1].data
47   #get qualities
48   @qualities = @directory_entries["PCON"][1].data
49   # get sample title
50   @sample_title = @directory_entries["SMPL"][1].data
51   @directory_entries["PDMF"].size > 2 ? @dye_mobility = @directory_entries["PDMF"][2].data : @dye_mobility = @directory_entries["PDMF"][1].data
52   #get trace data
53   @chemistry = @directory_entries["phCH"][1].data
54   base_order = @directory_entries["FWO_"][1].data.map{|char| char.chr.downcase}
55   (9..12).each do |data_index|
56     self.instance_variable_set("@#{base_order[data_index-9]}trace", @directory_entries["DATA"][data_index].data)
57   end
58 
59 end

Public Instance Methods

data(name, tag_number = 1) click to toggle source

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

   # File lib/bio/db/sanger_chromatogram/abif.rb
68 def data(name, tag_number = 1)
69   d = @directory_entries[name]
70   d ? d[tag_number].data : nil
71 end