bio-bigbio 0.1.1

data/lib/bigbio/sequence/predictorf.rb

@@ -0,0 +1,140 @@
+# ORF predictor class
+#
+
+require 'bigbio/sequence/translate'
+
+class ORFsequence
+  attr_accessor :seq
+  def initialize sequence
+    @seq = sequence
+  end
+end
+
+# Helper class for storing ORF information
+class ORFnucleotides < ORFsequence
+  attr_reader :start, :stop
+  def initialize sequence, start, stop
+    super(sequence)
+    @start = start
+    @stop = stop
+  end
+
+  def seq
+    @seq[@start..@stop-1]
+  end
+
+  def fullseq
+    @seq
+  end
+
+  def to_s
+    seq
+  end
+
+end
+
+# Helper class for storing ORF information
+class ORFaminoacids < ORFsequence
+end
+
+class ORF
+  attr_reader :id, :descr, :nt, :aa, :frame
+  def initialize num, type, id, descr, nt, frame, start, aa
+    @id = id.to_s + '_' + (num + 1).to_s
+    # ---- adjust start to match frame
+    start += frame.abs-1
+    # ---- stop should not go beyond sequence
+    stop = start + aa.size * 3
+    if stop > nt.size
+      stop = nt.size
+    end
+    # ---- if frame < 0 it should reverse complement
+    if frame < 0
+      nt = Bio::Sequence::NA.new(nt).reverse_complement.to_s.upcase
+    end
+    # p [start, stop, stop-start]
+    # p nt
+    fr = frame.to_s
+    fr = '+'+fr if frame > 0
+    @descr = "[#{type} #{fr} #{start} - #{stop}; #{stop-start}/#{nt.size}] " + descr
+    @nt = ORFnucleotides.new(nt, start, stop)
+    @frame = frame
+    @aa = ORFaminoacids.new(aa)
+  end
+
+  def <=> other
+    if frame == other.frame
+      nt.seq <=> other.nt.seq
+    else
+      frame <=> other.frame
+    end
+  end
+
+  def to_fastarec
+    aa = FastaRecord.new(@id,@descr,@aa.seq)
+    nt = FastaRecord.new(@id,@descr,@nt.seq)
+    FastaPairedRecord.new(nt,aa)
+  end
+end
+
+class PredictORF
+
+  include Bio::Big::FrameCodonHelpers 
+
+  def initialize id, descr, seq, trn_table
+    @id        = id
+    @descr     = descr
+    @seq       = seq.gsub(/\s/,'')
+    @trn_table = trn_table
+    @startcodons =  # FIXME: this should be linked properly
+      if trn_table == nil or trn_table == 0
+        START_CODONS
+      else # prokaryote
+        ['ATG','TTG','CTG','AUG','UUG','CUG']
+      end
+  end
+
+  # Return a list of predicted ORFs with :minsize AA's. The ORF's
+  # are between STOP codons (so sequences without a proper START codon 
+  # are included)
+  def stopstop minsize=30
+    type = "XX"
+    orfs = []
+    translate = Nucleotide::Translate.new(@trn_table)
+    aa_frames = translate.aa_6_frames(@seq)
+    # p @seq
+    # pp aa_frames
+    num = 0
+    aa_frames.each do | aa_frame |
+      frame = aa_frame[:frame]
+      aa = aa_frame[:sequence]
+      aa_start = 0
+      aa.split(/\*/).each do | candidate |
+        if candidate.size >= minsize and candidate.size > 0
+          orf = ORF.new(num,type,@id,@descr,@seq,frame,aa_start*3,candidate)
+          orfs.push orf
+          num += 1
+        end
+        aa_start += candidate.size + 1
+      end
+    end
+    orfs
+  end
+
+  # Return a list of predicted ORFs with :minsize AA's. The ORF's
+  # are between START and STOP codons (ATG, TTG, CTG and AUG, UUG and CUG for
+  # now, a later version should use the EMBOSS translation table).
+  def startstop minsize=30
+    stopstop(minsize).find_all { | orf | 
+      # p [orf.nt.seq[0..2].upcase,@startcodons.include?(orf.nt.seq[0..2].upcase)]
+      @startcodons.include?(orf.nt.seq[0..2].upcase)
+    }
+  end 
+
+  # Return the longest ORF that has a START codon (see +startstop+)
+  # Returns nil if none is found
+  def longest_startstop minsize=0
+    startstop(minsize).first
+  end
+    
+end

data/lib/bigbio/sequence/translate.rb

@@ -0,0 +1,52 @@
+
+module Nucleotide
+
+  module TranslationTable
+  end
+
+  class Translate
+
+    include Bio::Big::TranslationAdapter
+
+      # Table can be either an id (integer) or a Biolib::Emboss TrnTable
+
+    def initialize table 
+      table = 0 if table == nil
+      if table.kind_of? Numeric
+        @trn_table = Bio::Big::TranslationAdapter.translation_table(table)
+      else
+        @trn_table = table
+      end
+    end
+
+    # Return all six reading frames as an Array - ordered as
+    # frames [1,2,3,-1,-2,-3] with as tuples [frame, AAsequence].
+    #
+    # Note that the nucleotide sequence does not get modified.
+
+    def aa_6_frames seq
+      res = []
+      # remove white space
+      seq = seq.gsub(/\s/,'')
+      [1,2,3,-1,-2,-3].each do | frame |
+        aa = Bio::Big::TranslationAdapter.translate(@trn_table,frame,seq)
+        res.push({:frame => frame, :sequence => aa})
+      end
+      res
+    end
+    # Return all forward reading frames as an Array - ordered as
+    # frames [1,2,3] with as tuples [frame, AAsequence]
+
+    def aa_forward_frames seq
+      res = []
+      # remove white space
+      seq = seq.gsub(/\s/,'')
+      [1,2,3].each do | frame |
+        aa = Bio::Big::TranslationAdapter.translate(@trn_table,frame,seq)
+        res.push({:frame => frame, :sequence => aa})
+      end
+      res
+    end
+  end
+end
+

data/lib/bigbio.rb

@@ -0,0 +1,38 @@
+# BigBio libraries
+
+require 'bigbio/environment'
+
+# find local plugin installation, and use it when there
+rootpath = File.dirname(File.dirname(__FILE__))
+bio_logger_path = File.join(rootpath,'..','bioruby-logger','lib')
+if File.directory? bio_logger_path
+  $: << bio_logger_path
+  $stderr.print "bio-logger loaded directly\n"
+else
+  require "rubygems"
+  gem "bio-logger"
+end
+require 'bio-logger'
+
+log = Bio::Log::LoggerPlus.new('bigbio')
+Bio::Big::Environment.instance.log = log
+
+begin
+  require 'biolib/emboss'
+  Bio::Big::Environment.instance.biolib = true
+rescue LoadError
+  log.outputters = Bio::Log::Outputter.stderr
+  log.warn "BioLib functionality not loaded"
+end
+
+require 'bio'
+require 'bigbio/adapters/translate'
+require 'bigbio/db/emitters/fasta_emitter'
+require 'bigbio/db/emitters/orf_emitter'
+
+autoload :FastaReader, 'bigbio/db/fasta'
+autoload :FastaWriter, 'bigbio/db/fasta'
+autoload :FastaPairedReader, 'bigbio/db/fasta'
+autoload :FastaPairedWriter, 'bigbio/db/fasta'
+autoload :BlastClust, 'bigbio/db/blast'
+autoload :PredictORF, 'bigbio/sequence/predictorf'

data/spec/emitter_spec.rb

@@ -0,0 +1,265 @@
+
+require 'rspec'
+
+$: << "../lib"
+
+require 'bigbio'
+
+describe Bio::Big::FastaEmitter, "when using the emitter" do
+  include Bio::Big
+
+  it "should emit small parts" do
+    s = ""
+    FastaEmitter.new("test/data/fasta/nt.fa",10).emit_seq do | part, index, tag, seq |
+      # p [index, part, tag, seq]
+      s += seq
+      if index == 95 and part == :tail
+        s.should == "ATCATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGTCTTCAGTGTACAGTATCAAGGGCTCGATCTGCGGTGGATGAGACATCAGATTCAGGAGCTTTTCAAAGAACTGCATCGACATCCGTAACTTCGTTTCAAAAGATTCCAATTCTCAGTTTCAGCTGAATCTGGTAGATACCATCTTTACATATCGTATGCTTGTCATGGGCTTCTAGATGCCTTTCATACTTAAAGATCAAAGGACTTGACGATGCAATAAGCTTCTCGTCTGTAAAACCC"
+      end
+      s = "" if part == :tail
+    end
+  end
+
+  it "should emit large parts" do 
+    FastaEmitter.new("test/data/fasta/nt.fa").emit_seq do | part, index, tag, seq |
+      # p [index, part, tag, seq]
+      if index == 95
+        seq.should == "ATCATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGTCTTCAGTGTACAGTATCAAGGGCTCGATCTGCGGTGGATGAGACATCAGATTCAGGAGCTTTTCAAAGAACTGCATCGACATCCGTAACTTCGTTTCAAAAGATTCCAATTCTCAGTTTCAGCTGAATCTGGTAGATACCATCTTTACATATCGTATGCTTGTCATGGGCTTCTAGATGCCTTTCATACTTAAAGATCAAAGGACTTGACGATGCAATAAGCTTCTCGTCTGTAAAACCC"
+      end
+    end
+  end
+end
+
+describe Bio::Big::ShortFrameState, "when using the ShortFrameState" do
+
+  include Bio::Big
+  
+  it "should find an ORF" do
+    fr = ShortFrameState.new "atggattaaatgtaatggatttaatgtaaa",0,0
+    orfs = fr.get_stopstop_orfs
+    orfs.map{ | orf | orf.pos }.should == [ 3, 5 ]
+    orfs.map{ | orf | orf.to_seq }.should == ["ATGTAA", "TGGATTTAA"]
+    orfs = fr.get_startstop_orfs
+    orfs.map{ | orf | orf.pos }.should == [ 0, 3 ]
+    orfs.map{ | orf | orf.to_seq }.should == ["ATGGATTAA","ATGTAA"]
+  end
+  it "should handle min_size" do
+    fr = ShortFrameState.new "atggattaaatgtaatggatttaatgtaaa",0,9
+    orfs = fr.get_stopstop_orfs
+    orfs.map{ | orf | orf.to_seq }.should == [ "TGGATTTAA"]
+    orfs.map{ | orf | orf.pos }.should == [ 5 ]
+    fr.get_startstop_orfs.should == []
+  end
+  it "should find ORFs in" do
+    fr = ShortFrameState.new "atgttttaaatgtaatgttgttaaatgttttaaatgtaatgttgttaa",0,0
+    orfs = fr.get_stopstop_orfs
+    orfs.map{ | orf | orf.to_seq }.should ==  ["ATGTAA", "TGTTGTTAA", "ATGTTTTAA", "ATGTAA", "TGTTGTTAA"]
+    orfs.map{ | orf | orf.pos }.should == [3, 5, 8, 11, 13]
+    orfs = fr.get_startstop_orfs
+    orfs.map{ | orf | orf.to_seq }.should == ["ATGTTTTAA", "ATGTAA", "ATGTTTTAA", "ATGTAA"]
+    orfs.map{ | orf | orf.pos }.should == [ 0, 3, 8, 11]
+  end
+
+  it "should match results of EMBOSS getorf" do
+    s = "AG GTTCGNACGGTCATCGNATNAAGTCTTGNATATCG TAA TTNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTG GGG AAAACTTTG TGA GCAAAGAGCGAGAAAATGAGCGGANCGG TAA GAAAATCGCGGATGTGGCTTTCAAAGCTTCAAGGACTATCGATTGGGATGGTATGGC TAA GGTCCTTGTCACAGATGAGGCTCGTAGAG".gsub(/ /,'')
+    # >_3 [3 - 167] #0
+    # 1st  GTTCGNACGGTCATCGNATNAAGTCTTGNATATCGTAATTNCGCGTGCCGCCTTCTTTCT
+    # CCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCA
+    # GTGTGTGTATTTTGGGGAAAACTTTGTGAGCAAAGAGCGAGAAAA
+    # >_4 [171 - 179] #0
+    # OK   GCGGANCGG
+    # >_5 [183 - 239] #0
+    # OK   GAAAATCGCGGATGTGGCTTTCAAAGCTTCAAGGACTATCGATTGGGATGGTATGGC
+    # >_6 [243 - 257] #0
+    # OK-  GGTCCTTGTCACAGA
+    # >_7 [261 - 266] #0
+    # OK-  GGCTCGTAG
+    # >_8 [1 - 270] # 1
+    # whole!  AGGTTCGNACGGTCATCGNATNAAGTCTTGNATATCGTAATTNCGCGTGCCGCCTTCTTT
+    # CTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGT
+    # CAGTGTGTGTATTTTGGGGAAAACTTTGTGAGCAAAGAGCGAGAAAATGAGCGGANCGGT
+    # AAGAAAATCGCGGATGTGGCTTTCAAAGCTTCAAGGACTATCGATTGGGATGGTATGGCT
+    # AAGGTCCTTGTCACAGATGAGGCTCGTAGA
+    # >_1 [2 - 37] #2
+    # 1st-   GGTTCGNACGGTCATCGNATNAAGTCTTGNATATCG
+    # >_2 [41 - 148] #2
+    # OK-   TTNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCT
+    # TCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTG
+    # >_9 [152 - 271] #2
+    # last- CAAAGAGCGAGAAAATGAGCGGANCGGTAAGAAAATCGCGGATGTGGCTTTCAAAGCTT
+    # CAAGGACTATCGATTGGGATGGTATGGCTAAGGTCCTTGTCACAGATGAGGCTCGTAGAG
+
+    # Frame 0
+    minsize = 0
+    fr = ShortFrameState.new s,0,minsize
+    orfs = fr.get_stopstop_orfs
+    orfs.map{ | orf | orf.to_seq }.should == []
+
+    # Frame 1
+    fr = ShortFrameState.new s[1..-1],0,minsize
+    os = fr.get_stopstop_orfs
+    os.map{ | orf | orf.to_seq }.should == ["TTNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTGTGA"]
+    orfs += os
+    # Frame 2
+    fr = ShortFrameState.new s[2..-1],0,minsize
+    os = fr.get_stopstop_orfs
+    os.map{ | orf | orf.to_seq }.should == ["GCGGANCGGTAA", "GAAAATCGCGGATGTGGCTTTCAAAGCTTCAAGGACTATCGATTGGGATGGTATGGCTAA", "GGTCCTTGTCACAGATGA", "GGCTCGTAG"]
+    orfs += os
+    orfs.size.should == 5
+
+    # >_1 [235 - 270] 
+    # Last: ATGGCTAAGGTCCTTGTCACAGATGAGGCTCGTAGA
+    # >_2 [167 - 271] 
+    # Last: ATGAGCGGANCGGTAAGAAAATCGCGGATGTGGCTTTCAAAGCTTCAAGGACTATCGATT
+    # GGGATGGTATGGCTAAGGTCCTTGTCACAGATGAGGCTCGTAGAG
+
+    # Frame 0
+    minsize = 0
+    fr = ShortFrameState.new s,0,minsize
+    orfs = fr.get_startstop_orfs
+
+    # Frame 1
+    fr = ShortFrameState.new s[1..-1],0,minsize
+    orfs += fr.get_startstop_orfs
+    # Frame 2
+    fr = ShortFrameState.new s[2..-1],0,minsize
+    orfs += fr.get_startstop_orfs
+    orfs.map{ | orf | orf.to_seq }.should == []
+    orfs.size.should == 0
+  end
+end
+
+describe Bio::Big::ShortFrameState, "when combining frames" do
+  include Bio::Big
+  it "should combine a forward frame" do
+    s1 = "atggattaaatgtaata"
+    s2 = "atggatttaatgtaaa"
+    fr = ShortFrameState.new s1,0,0
+    fr.ntseq_pos.should == 0
+    orfs = fr.get_stopstop_orfs
+    orfs.size == 1 # in codons
+    fr3 = FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
+    fr3.ntseq_pos.should == 15
+    fr3.codons.to_seq.should == "TAATGGATTTAATGTAAA"
+    norfs = fr3.get_stopstop_orfs
+    orfs += norfs
+    orfs.map{ | orf | orf.to_seq }.should == ["ATGTAA", "TGGATTTAA"]
+    orfs.map{ | orf | orf.track_ntseq_pos }.should == [9,18]
+  end
+
+  it "should combine a forward frame without ORFs in first seq" do
+    s1 = "atggattaaatgta"
+    #     ......---===xx
+    s2 = "atggatttaattattataaa"
+    #     x======xxx======xxx.
+    fr = ShortFrameState.new s1,0,0
+    fr.ntseq_pos.should == 0
+    orfs = fr.get_stopstop_orfs
+    orfs.size == 0 # in codons
+    fr3 = FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
+    fr3.ntseq_pos.should == 0
+    fr3.codons.to_seq.should == "ATGGATTAAATGTAATGGATTTAATTATTATAA"
+    norfs = fr3.get_stopstop_orfs
+    orfs = norfs
+    orfs.map{ | orf | orf.to_seq }.should == ["ATGTAA","TGGATTTAA","TTATTATAA"]
+    orfs.map{ | orf | orf.track_ntseq_pos }.should == [9,9+6,9+6+9]
+  end
+
+  it "should combine a forward frame without ORFs in first seq" do
+    s1 = "atggattaaatgta"
+    #     ......---===xx
+    s2 = "atggatttaatgtaaa"
+    #     x======xxx
+    fr = ShortFrameState.new s1,0,0
+    fr.ntseq_pos.should == 0
+    orfs = fr.get_stopstop_orfs
+    orfs.size == 0 # in codons
+    fr3 = FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
+    # p fr3
+    fr3.ntseq_pos.should == 0 # on the combined sequences
+    fr3.codons.to_seq.should == "ATGGATTAAATGTAATGGATTTAATGTAAA"
+    norfs = fr3.get_stopstop_orfs
+    orfs += norfs
+    orfs.map{ | orf | orf.to_seq }.should == ["ATGTAA", "TGGATTTAA"]
+    orfs.map{ | orf | orf.track_ntseq_pos }.should == [9,9+6]
+  end
+
+  it "should combine a reverse frame" do
+    # Reversed (real locations on contig):
+    #
+    # |  3                21  B |
+    # ttaaatgtaatttaggtaaatttat atgtaaattaggta (reversed)
+    # ...^--============xxx^=======xxx
+    #       ^                     ^
+    # Actual feed:
+    #
+    # s2=              s1=
+    # 18                 0 (ntseq_pos)
+    # "atggattaaatgta" "tatttaaatggatttaatgtaaatt"
+    #  ......xxx=====   ~===xx^============--^...                               
+    #  0  1  2  3        0  1  2  3 
+
+    s2 = "tatttaaatggatttaatgtaaatt"
+    #     ~===xx^============--^...                               
+    s1 = "atggattaaatgta"
+    #     ......xxx=====
+    # now move the other way, as sequences get emitted on the left
+    fr = ShortReversedFrameState.new s2,0,0
+    # p fr
+    fr.codons.to_seq.should == "ATTTAAATGGATTTAATGTAAATT"
+    fr.ntseq_pos.should == 0
+    orfs = fr.get_stopstop_orfs
+    orfs.map{ | orf | orf.to_seq }.should == ["ATGGATTTAATGTAA"]
+    orfs.first.pos.should == 2 # in codons
+    fr3 = FrameCodonHelpers::CreateShortFrame.create_left(fr,orfs,s1)
+    fr3.ntseq_pos.should == 18 # 6 codons
+    fr3.codons.to_seq.should == "ATGGATTAAATGTATATTTAA"
+    norfs = fr3.get_stopstop_orfs
+    orfs += norfs
+    orfs.map{ | orf | orf.to_seq }.should == ["ATGGATTTAATGTAA", "ATGTATATTTAA"]
+    orfs.map{ | orf | orf.pos }.should == [2,3]
+    orfs.map{ | orf | orf.track_ntseq_pos }.should == [6,18+9]
+  end
+
+end
+
+describe Bio::Big::OrfEmitter, "when using the ORF emitter" do
+  include Bio::Big
+
+  it "should emit STOP-STOP ORFs in all frames" do
+    f = FastaEmitter.new("test/data/fasta/nt.fa")
+    seqs = []
+    OrfEmitter.new(f,:stopstop)::emit_seq do | frame, index, tag, pos, seq |
+      break if index != 0
+      if frame == 0 and index == 0 and pos == 39
+        seq.should == "TTNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTGTGA"
+        # p [frame,index, tag, pos, seq]
+      end
+      if index == 0
+        seqs.push seq
+      end
+    end
+    seqs.join(';')[50..350].should == "TNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTGTGA;GCAAAGAGCGAGAAAATGAGCGGANCGGTAAGAAAATCGCGGATGTGGCTTTCAAAGCTTCAAGGACTATCGATTGGGATGGTATGGCTAAGGTCCTTGTCACAGATGAGGCTCGTAGAGAGTTCTCTAACCTTCGTCGTGCTTTCGATGAGGTTAACACACAGCTCCAGACCAAATTTAGTCAGGACCT"
+  end
+  it "should emit STOP-STOP ORFs in all frames using a shorter emitter" do
+    f = FastaEmitter.new("test/data/fasta/nt.fa",150)
+    seqs = []
+    OrfEmitter.new(f,:stopstop)::emit_seq do | frame, index, tag, pos, seq |
+      break if index != 0
+      if frame == 0 and index == 0 and pos == 39
+        seq.should == "TTNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTGTGA"
+        # p [frame,index, tag, pos, seq]
+      end
+      if index == 0
+        seqs.push seq
+      end
+    end
+    # seqs.join(';')[50..350].should == "TNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTGTGA;GCAAAGAGCGAGAAAATGAGCGGANCGGTAAGAAAATCGCGGATGTGGCTTTCAAAGCTTCAAGGACTATCGATTGGGATGGTATGGCTAAGGTCCTTGTCACAGATGAGGCTCGTAGAGAGTTCTCTAACCTTCGTCGTGCTTTCGATGAGGTTAACACACAGCTCCAGACCAAATTTAGTCAGGACCT"
+  end
+  if false
+  it "should emit START-STOP ORFs in all frames"
+  it "should emit ORFs on any filter"
+  it "should emit ORFs using a minimum size"
+  it "should emit ORFs with adjoining sequences"
+  end
+end

data/spec/predictorf_spec.rb

@@ -0,0 +1,199 @@
+
+$: << "../lib"
+ENV['DATA'] = '../test/data/EMBOSS'
+
+require 'bigbio'
+
+# Note that PredictORF, at this point, leaves trailing X's for the AA sequence
+
+describe PredictORF, " when using a short simple nucleotide sequence" do
+  before :all do 
+    # initialize
+    id = 'test'
+    descr = 'Test'
+    # sequence = 'AGCTGAATCTGGTAGATACCATCTTTAA'
+    sequence = 'AGCTGAATCTGG'
+    # trn_table = Biolib::Emboss.ajTrnNewI(1)
+    trn_table = Bio::Big::TranslationAdapter.translation_table(1)
+  
+    @predictorf = PredictORF.new(id,descr,sequence,trn_table)
+    @orflist = @predictorf.stopstop(0)
+    # @orflist.each do | orf | p [orf.descr,orf] end
+  end
+
+  it "stopstop(0) should render six reading frames and seven ORF" do
+    # >EMBOSS_001_1
+    # S*IW
+    # >EMBOSS_001_2
+    # AESG
+    # >EMBOSS_001_3
+    # LNLX
+    # >EMBOSS_001_4
+    # PDSA
+    # >EMBOSS_001_5
+    # RFSX
+    # >EMBOSS_001_6
+    # QIQL
+    @orflist[0].aa.seq.should == "S"
+    @orflist[3].aa.seq[0..2].should == "LNL"
+    @orflist[4].aa.seq[0..2].should == "PDS"
+    @orflist.size.should == 7
+  end
+
+  # frame +1 - 4 codons S*IW 
+  it "should give a first valid +1 frame" do
+    orf = @orflist[1]
+    orf.frame.should == 1
+    orf.nt.start.should == 6
+    orf.aa.seq.should == "IW"
+    orf.nt.seq.should == "ATCTGG"
+  end
+
+  # frame +1 - 4 codons S*IW 
+  it "should give a second valid +1 frame" do
+    orf = @orflist[0]
+    orf.frame.should equal 1
+    orf.nt.start.should equal 0
+    orf.aa.seq.should == "S"
+    orf.nt.seq.should == "AGC"
+  end
+
+  # frame +2 - 3 codons AES
+  it "should give a valid +2 frame" do 
+    orf = @orflist[2]
+    # pp @orflist
+    # pp orf
+    orf.nt.seq[0..8].should == "GCTGAATCT"
+    orf.frame.should == 2
+    orf.nt.start.should == 1
+    # orf.nt.stop.should == 12 - EMBOS differs
+    orf.aa.seq[0..2].should == "AES"
+  end
+
+  # frame +3 - 3 codons LNL
+  it "should give a valid +3 frame" do
+    orf = @orflist[3]
+    orf.frame.should == 3
+    orf.nt.start.should == 2
+    # orf.nt.stop.should == 12
+    orf.aa.seq[0..3].should == "LNL"
+    orf.nt.seq[0..9].should == "CTGAATCTG"
+  end
+
+  # frame -1 - 4 codons PDSA 
+  it "should give a valid -1 frame" do
+    orf = @orflist[4]
+    orf.frame.should == -1
+    orf.nt.start.should == 0
+    orf.nt.stop.should == 12
+    orf.aa.seq.should == "PDSA"
+    orf.nt.seq.should == "CCAGATTCAGCT"
+  end
+
+  # frame -2 - 3 codons RFSX
+  it "should give a valid -3 frame" do
+    orf = @orflist[5]
+    orf.frame.should == -2
+    orf.nt.start.should == 1
+    # orf.nt.stop.should == 12
+    orf.aa.seq[0..2].should == "RFS"
+    orf.nt.seq[0..8].should == "CAGATTCAG"
+  end
+
+  # frame -3 - 3 codons QIQL
+  it "should give a valid -3 frame" do
+    orf = @orflist[6]
+    orf.frame.should == -3
+    orf.nt.start.should == 2
+    # orf.nt.stop.should == 12
+    orf.aa.seq[0..2].should == "QIQ"
+    orf.nt.seq[0..8].should == "AGATTCAGC"
+  end
+end
+
+describe PredictORF, " when using a more complicated nucleotide sequence" do
+  before :all do 
+    # initialize
+    id = "PUT-157a-Arabidopsis_thaliana-126"
+    descr = "PlantGDB Arabidopsis_thaliana Jan_15_2007"
+    sequence = "ATCATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGT
+                CTTCAGTGTACAGTATCAAGGGCTCGATCTGCGGTGGATGAGACATCAGATTCAGGAGCT
+                TTTCAAAGAACTGCATCGACATCCGTAACTTCGTTTCAAAAGATTCCAATTCTCAGTTTC
+                AGCTGAATCTGGTAGATACCATCTTTACATATCGTATGCTTGTCATGGGCTTCTAGATGC
+                CTTTCATACTTAAAGATCAAAGGACTTGACGATGCAATAAGCTTCTCGTCTGTAAAACCC"
+    # @trn_table = Biolib::Emboss.ajTrnNewI(1)
+    @trn_table = Bio::Big::TranslationAdapter.translation_table(1)
+    @predictorf = PredictORF.new(id,descr,sequence,@trn_table)
+    @orflist = @predictorf.stopstop(0)
+    # @orflist.each_with_index do | orf,i | p [i,orf.descr,orf.aa.seq,orf.nt.seq] end
+    # >EMBOSS_001_1
+    # IISNTSFLSLASKFTTRGSRLQCTVSRARSAVDETSDSGAFQRTASTSVTSFQKIPILSF
+    # S*IW*IPSLHIVCLSWASRCLSYLKIKGLDDAISFSSVKP
+    # >EMBOSS_001_2
+    # SLATPASSLSLQSSLLVDLVFSVQYQGLDLRWMRHQIQELFKELHRHP*LRFKRFQFSVS
+    # AESGRYHLYISYACHGLLDAFHT*RSKDLTMQ*ASRL*N
+    # >EMBOSS_001_3
+    # H*QHQLPLSRFKVHYSWISSSVYSIKGSICGG*DIRFRSFSKNCIDIRNFVSKDSNSQFQ
+    # LNLVDTIFTYRMLVMGF*MPFILKDQRT*RCNKLLVCKT
+    # >EMBOSS_001_4
+    # GFYRREAYCIVKSFDL*V*KASRSP*QAYDM*RWYLPDSAETENWNLLKRSYGCRCSSLK
+    # SS*I*CLIHRRSSP*YCTLKTRSTSSEL*SEREEAGVAND
+    # >EMBOSS_001_5
+    # VLQTRSLLHRQVL*SLSMKGI*KPMTSIRYVKMVSTRFS*N*ELESFETKLRMSMQFFEK
+    # LLNLMSHPPQIEPLILYTEDEIHE**TLKRERGSWCC**X
+    # >EMBOSS_001_6
+    # GFTDEKLIASSSPLIFKYERHLEAHDKHTICKDGIYQIQLKLRIGIF*NEVTDVDAVL*K
+    # APESDVSSTADRALDTVH*RRDPRVVNFEARERKLVLLMX
+  end
+  it "stopstop(0) should render ORFs" do
+    @orflist[0].aa.seq[0..3].should == "IISN"
+    @orflist[13].aa.seq[0..3].should == "GFYR"
+    @orflist[22].aa.seq[0..3].should == "VLQT"
+  end
+  it "stopstop(0) should render 33 reading frames and seven ORF" do
+    @orflist.size.should == 32
+  end
+  it "startstop(30) should render ORFs starting with a start codon" do
+    orflist = @predictorf.startstop(5)
+    # orflist.each do | orf | p [orf.descr,orf] end
+    orflist[0].aa.seq.should == "MPFILKDQRT"
+    orflist.size.should == 1
+  end
+  it "should never return an empty sequence" do
+    orflist = @predictorf.stopstop(0)
+    orflist.each do | orf |
+      orf.nt.seq.size.should >= 0
+    end
+  end
+
+  it "should return 3 sequences when the minsize is 132" do
+    orflist = @predictorf.stopstop(44)
+    orflist.size.should == 4
+  end
+
+  it "should return 2 sequences when the minsize is 133" do
+    orflist = @predictorf.stopstop(45)
+    orflist.size.should == 3
+  end
+
+  it "should have -1 frame" do
+    sequence = "ATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGT"
+    # >EMBOSS_001_4
+    # TRSTSSEL*SEREEAGVAN
+    predictorf = PredictORF.new('test','TEST',sequence,@trn_table)
+    orflist = predictorf.stopstop(0)
+    # orflist.each_with_index do | orf,i | p [i,orf.descr,orf.aa.seq,orf.nt.seq] end
+    orflist[2].aa.seq[0..18].should == "QHQLPLSRFKVHYSWIS"
+  end
+
+  it "should correctly handle a sequence starting with a STOP codon" do
+    sequence = "ATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGT"
+    # >EMBOSS_001_3
+    # *QHQLPLSRFKVHYSWIS
+    predictorf = PredictORF.new('test','TEST',sequence,@trn_table)
+    orflist = predictorf.stopstop(0)
+    # orflist.each_with_index do | orf,i | p [i,orf.descr,orf.aa.seq,orf.nt.seq] end
+    orflist[2].aa.seq[0..18].should == "QHQLPLSRFKVHYSWIS"
+  end
+
+end