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)

Source

   # 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

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

Public Instance Methods

data (name, tag_number = 1)

Source

   # 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

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