Class: Bio::SangerChromatogram

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/db/sanger_chromatogram/chromatogram.rb

Overview

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

Direct Known Subclasses

Abif, Scf

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#atrace ⇒ Object

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



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 63

def atrace
  @atrace
end

#chromatogram_type ⇒ Object

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



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 53

def chromatogram_type
  @chromatogram_type
end

#ctrace ⇒ Object

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



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 65

def ctrace
  @ctrace
end

#dye_mobility ⇒ Object

The mobility of the dye used when sequencing (String)



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 71

def dye_mobility
  @dye_mobility
end

#gtrace ⇒ Object

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



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 67

def gtrace
  @gtrace
end

#peak_indices ⇒ Object

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



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 61

def peak_indices
  @peak_indices
end

#qualities ⇒ Object

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



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 59

def qualities
  @qualities
end

#sequence ⇒ Object

The sequence contained within the chromatogram (String)



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 57

def sequence
  @sequence
end

#ttrace ⇒ Object

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



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 69

def ttrace
  @ttrace
end

#version ⇒ Object

The Version of the Scf or Abif file (String)



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 55

def version
  @version
end

Class Method Details

.open(filename) ⇒ Object 



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 73

def self.open(filename)
  Bio::FlatFile.open(self, filename)
end

Instance Method Details

#complement ⇒ Object

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



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 126

def complement
  chromatogram = self.dup
  chromatogram.complement!
  return chromatogram
end

#complement! ⇒ Object

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



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 95

def complement!
  # reverse traces
  tmp_trace = @atrace
  @atrace = @ttrace.reverse
  @ttrace = tmp_trace.reverse
  tmp_trace = @ctrace
  @ctrace = @gtrace.reverse
  @gtrace = tmp_trace.reverse

  # reverse base qualities
  if (defined? @aqual) && @aqual # if qualities exist
    tmp_qual = @aqual
    @aqual = @tqual.reverse
    @tqual = tmp_qual.reverse
    tmp_qual = @cqual
    @cqual = @gqual.reverse
    @gqual = tmp_qual.reverse
  end

  #reverse qualities
  @qualities = @qualities.reverse

  #reverse peak indices
  @peak_indices = @peak_indices.map{|index| @atrace.size - index}
  @peak_indices.reverse!

  # reverse sequence
  @sequence = @sequence.reverse.tr('atgcnrykmswbvdh','tacgnyrmkswvbhd')
end

#seq ⇒ Object

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



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 78

def seq
  Bio::Sequence::NA.new(@sequence)
end

#sequence_string ⇒ Object

Returns the sequence from the chromatogram as a string



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 89

def sequence_string
  @sequence
end

#to_biosequence ⇒ Object Also known as: to_seq

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



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# File 'lib/bio/db/sanger_chromatogram/chromatogram.rb', line 83

def to_biosequence
  Bio::Sequence.adapter(self, Bio::Sequence::Adapter::SangerChromatogram)
end