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No matching classes.

# 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) click to toggle source

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

### Public Instance Methods

complement() click to toggle source

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

    # File lib/bio/db/sanger_chromatogram/chromatogram.rb, line 127
    def complement
      chromatogram = self.dup
      chromatogram.complement!
      return chromatogram
    end

complement!() click to toggle source

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

    # File lib/bio/db/sanger_chromatogram/chromatogram.rb, line 96
    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 !@aqual.nil? # 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() click to toggle source

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

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

sequence_string() click to toggle source

Returns the sequence from the chromatogram as a string

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

to_biosequence() click to toggle source

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

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

Also aliased as: to_seq
to_seq() click to toggle source
Alias for: to_biosequence

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