class Bio::SangerChromatogram

Description¶ ↑

This is the Superclass for the Abif and Scf classes that allow importing of the common scf and abi sequence chromatogram formats The following attributes are Common to both the Abif and Scf subclasses

chromatogram_type (String): This is extracted from the chromatogram file itself and will probably be either .scf or ABIF for Scf and Abif files respectively.
version (String): The version of the Scf or Abif file
sequence (String): the sequence contained within the chromatogram as a string.
qualities (Array): the quality scores of each base as an array of integers. These will probably be phred scores.
peak_indices (Array): if the sequence traces contained within the chromatogram are imagined

as being plotted on an x,y graph, the peak indices are the x positions of the peaks that

represent the nucleotides bases found in the sequence from the chromatogram. For example if

the peak_indices are [16,24,37,49 .…] and the sequence is AGGT.…, at position 16 the

traces in the chromatogram were base-called as an A, position 24 a G, position 37 a G, position 49 a T etc
atrace, ctrace, gtrace, ttrace (Array): If the sequence traces contained within the chromatogram are imagined as being plotted on an x,y graph, these attributes are arrays of y positions for each of the 4 nucleotide bases along the length of the x axis. If these were plotted joined by lines of different colours then the resulting graph should look like the original chromatogram file when viewed in a chromtogram viewer such as Chromas, 4Peaks or FinchTV.
dye_mobility (String): The mobility of the dye used when sequencing. This can influence the base calling

Usage¶ ↑

filename = "path/to/sequence_chromatogram_file"

for Abif files

chromatogram_ff = Bio::Abif.open(filename)

for Scf files

chromatogram_ff = Bio::Scf.open(filename)

chromatogram = chromatogram_ff.next_entry
chromatogram.to_seq # => returns a Bio::Sequence object
chromatogram.sequence # => returns the sequence contained within the chromatogram as a string
chromatogram.qualities # => returns an array of quality values for each base
chromatogram.atrace # => returns an array of the a trace y positions

Attributes

atrace [RW]

An array of ‘y’ positions (see description) for the ‘A’ trace from the chromatogram (Array

chromatogram_type [RW]

The type of chromatogram file .scf for Scf files and ABIF doe Abif files

ctrace [RW]

An array of ‘y’ positions (see description) for the ‘C’ trace from the chromatogram (Array

dye_mobility [RW]

The mobility of the dye used when sequencing (String)

gtrace [RW]

An array of ‘y’ positions (see description) for the ‘G’ trace from the chromatogram (Array

peak_indices [RW]

An array ‘x’ positions (see description) on the trace where the bases occur/have been called (Array)

qualities [RW]

An array of quality scores for each base in the sequence (Array)

sequence [RW]

The sequence contained within the chromatogram (String)

ttrace [RW]

An array of ‘y’ positions (see description) for the ‘T’ trace from the chromatogram (Array

version [RW]

The Version of the Scf or Abif file (String)

Public Class Methods

open (filename)

Source

   # File lib/bio/db/sanger_chromatogram/chromatogram.rb
73 def self.open(filename)
74   Bio::FlatFile.open(self, filename)
75 end

Public Instance Methods

complement ()

Source

    # File lib/bio/db/sanger_chromatogram/chromatogram.rb
126 def complement
127   chromatogram = self.dup
128   chromatogram.complement!
129   return chromatogram
130 end

Returns a new chromatogram object of the appropriate subclass (scf or abi) where the sequence, traces and qualities have all been revesed and complemented

complement! ()

Source

    # File lib/bio/db/sanger_chromatogram/chromatogram.rb
 95 def complement!
 96   # reverse traces
 97   tmp_trace = @atrace
 98   @atrace = @ttrace.reverse
 99   @ttrace = tmp_trace.reverse
100   tmp_trace = @ctrace
101   @ctrace = @gtrace.reverse
102   @gtrace = tmp_trace.reverse
103 
104   # reverse base qualities
105   if (defined? @aqual) && @aqual # if qualities exist
106     tmp_qual = @aqual
107     @aqual = @tqual.reverse
108     @tqual = tmp_qual.reverse
109     tmp_qual = @cqual
110     @cqual = @gqual.reverse
111     @gqual = tmp_qual.reverse
112   end
113 
114   #reverse qualities
115   @qualities = @qualities.reverse
116 
117   #reverse peak indices
118   @peak_indices = @peak_indices.map{|index| @atrace.size - index}
119   @peak_indices.reverse!
120 
121   # reverse sequence
122   @sequence = @sequence.reverse.tr('atgcnrykmswbvdh','tacgnyrmkswvbhd')
123 end

Reverses and complements the current chromatogram object including its sequence, traces and qualities

seq ()

Source

   # File lib/bio/db/sanger_chromatogram/chromatogram.rb
78 def seq
79   Bio::Sequence::NA.new(@sequence)
80 end

Returns a Bio::Sequence::NA object based on the sequence from the chromatogram

sequence_string ()

Source

   # File lib/bio/db/sanger_chromatogram/chromatogram.rb
89 def sequence_string
90   @sequence
91 end

Returns the sequence from the chromatogram as a string

to_biosequence ()

Source

   # File lib/bio/db/sanger_chromatogram/chromatogram.rb
83 def to_biosequence
84   Bio::Sequence.adapter(self, Bio::Sequence::Adapter::SangerChromatogram)
85 end

Returns a Bio::Sequence object based on the sequence from the chromatogram

Also aliased as: to_seq

to_seq ()

Alias for: to_biosequence