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absee has underwent a lot of structural changes.

First, it only retrieves the information you want instead of returning all traces and called bases.
Second, it’s a class now, so you can hold onto multiple sequencing data.
Third, it now has quality scores.

%irb
>> require ‘absee’
=> true
>> my_variable = ABSee.new()
=> #<ABSee:0x000001008599d0>
>> my_variable.read("/Users/Jenny/Desktop/my_sequence.ab1")
=> nil
>> my_variable.get_calledSequence()

Class Methods

  • read(file_location)
    • returns nil
  • get_traceA()
    • returns an array with the trace data for adenine
  • get_traceG()
    • returns an array with the trace data for guanine
  • get_traceC()
    • returns an array with the trace data for cytosine
  • get_traceT()
    • returns an array with the trace data for thymine
  • get_calledSequence()
    • returns an array with the Basecalled sequence
  • get_qualityScores()
    • returns an array with the Basecalled quality scores
  • get_peakIndexes()
      returns an array with indexes of the called sequence in the trace

[updated again as a Ruby class]

absee has an update!

The 0.1.0.0 version now encapsulates the methods in a Ruby Module, instead of being global functions.

Example usage:

% irb
>> require ‘absee’
=> true
>> Absee.readAB(“/Users/Jenny/Desktop/my_sequence.ab1″)

It still returns six arrays (the trace values for ACGT, called sequence, and peak indexes).

More information can be found on my previous post.

Thanks goes to Dan Cahoon for forking my absee on github.