Contents

require File.expand_path( File.dirname(__FILE__) + '/spec_helper' )
require 'sample_enzyme'
require 'set'

describe SampleEnzyme, "digesting sequences" do
  it 'can digest with no missed cleavages' do
    st = "CRGATKKTAGRPMEK"
    SampleEnzyme.tryptic(st).should == %w(CR GATK K TAGRPMEK)
    st = "CATRP"
    SampleEnzyme.tryptic(st).should == %w(CATRP)
    st = "RCATRP"
    SampleEnzyme.tryptic(st).should == %w(R CATRP)
    st = ""
    SampleEnzyme.tryptic(st).should == []
    st = "R"
    SampleEnzyme.tryptic(st).should == %w(R)
  end

  it 'can digest with missed cleavages' do
    st = "CRGATKKTAGRPMEKLLLERTKY"
    zero = %w(CR GATK K TAGRPMEK LLLER TK Y)
    SampleEnzyme.tryptic(st,0).to_set.should == zero.to_set
    one = %w(CRGATK GATKK KTAGRPMEK TAGRPMEKLLLER LLLERTK TKY)
    SampleEnzyme.tryptic(st,1).to_set.should == (zero+one).to_set
    two = %w(CRGATKK GATKKTAGRPMEK KTAGRPMEKLLLER TAGRPMEKLLLERTK LLLERTKY)
    all = zero + one + two
    SampleEnzyme.tryptic(st,2).to_set.should == all.to_set
  end

  it 'contains duplicates IF there are duplicate tryptic sequences' do
    st = "AAAAKCCCCKDDDDKCCCCK"
    peps = SampleEnzyme.new('trypsin').digest(st, 2)
    peps.select {|aaseq| aaseq == 'CCCCK'}.size.should == 2
  end

  
end

Version data entries

2 entries across 2 versions & 1 rubygems

Version	Path
mspire-0.3.0	specs/sample_enzyme_spec.rb
mspire-0.3.1	specs/sample_enzyme_spec.rb