bio-gff3 0.6.0

data/lib/bio/system/lruhash.rb

@@ -0,0 +1,268 @@
+# LRU based Hash by Robert Klemme
+#
+# Copied from http://github.com/rklemme/muppet-laboratories
+#
+# License: unclear, not in repository, need to ask Permission
+# Added by Pjotr Prins (pjotr.prins@thebird.nl)
+
+require 'enumerator'
+
+# Hash with LRU expiry policy.  There are at most max_size elements in a
+# LruHash.  When adding more elements old elements are removed according
+# to LRU policy.
+class LRUHash
+  include Enumerable
+
+  attr_reader :max_size
+  attr_accessor :default, :default_proc, :release_proc
+
+  def initialize(max_size, default_value = nil, &block)
+    @max_size = normalize_max(max_size)
+    @default = default_value
+    @default_proc = block
+
+    @h = {}
+    @head = Node.new
+    @tail = front(Node.new)
+  end
+
+  def each_pair
+    if block_given?
+      each_node do |n|
+        yield [n.key, n.value]
+      end
+    else
+      enum_for :each_pair
+    end
+  end
+
+  alias each each_pair
+
+  def each_key
+    if block_given?
+      each_node do |n|
+        yield n.key
+      end
+    else
+      enum_for :each_key
+    end
+  end
+
+  def each_value
+    if block_given?
+      each_node do |n|
+        yield n.value
+      end
+    else
+      enum_for :each_value
+    end
+  end
+
+  def size
+    @h.size
+  end
+
+  def empty?
+    @head.succ.equal? @tail
+  end
+
+  def fetch(key, &b)
+    n = @h[key]
+
+    if n
+      front(n).value
+    else
+      (b || FETCH)[key]
+    end
+  end
+
+  def [](key)
+    fetch(key) do |k|
+      @default_proc ? @default_proc[self, k] : default
+    end
+  end
+
+  def keys
+    @h.keys
+  end
+
+  def values
+    @h.map {|k,n| n.value}
+  end
+
+  def has_key?(key)
+    @h.has_key? key
+  end
+
+  alias key? has_key?
+  alias member? has_key?
+  alias include? has_key?
+
+  def has_value?(value)
+    each_pair do |k, v|
+      return true if value.eql? v
+    end
+
+    false
+  end
+
+  alias value? has_value?
+
+  def values_at(*key_list)
+    key_list.map {|k| self[k]}
+  end
+
+  def assoc(key)
+    n = @h[key]
+
+    if n
+      front(n)
+      [n.key, n.value]
+    end
+  end
+
+  def rassoc(value)
+    each_node do |n|
+      if value.eql? n.value
+        front(n)
+        return [n.key, n.value]
+      end
+    end
+    nil
+  end
+
+  def key(value)
+    pair = rassoc(value) and pair.first
+  end
+
+  def store(key, value)
+    # same optimization as in Hash
+    key = key.dup.freeze if String === key && !key.frozen?
+
+    n = @h[key]
+
+    unless n
+      if size == max_size
+        # reuse node to optimize memory usage
+        n = delete_oldest
+        n.key = key
+        n.value = value
+      else
+        n = Node.new key, value
+      end
+
+      @h[key] = n
+    end
+
+    front(n).value = value
+  end
+
+  alias []= store
+
+  def delete(key)
+    n = @h[key] and remove_node(n).value
+  end
+
+  def delete_if
+    each_node do |n|
+      remove_node n if yield n.key, n.value
+    end
+  end
+
+  def max_size=(limit)
+    limit = normalize_max(limit)
+
+    while size > limit
+      delete_oldest
+    end
+
+    @max_size = limit
+  end
+
+  def clear
+    until empty?
+      delete_oldest
+    end
+
+    self
+  end
+
+  def to_s
+    s = nil
+    each_pair {|k, v| (s ? (s << ', ') : s = '{') << k.to_s << '=>' << v.to_s}
+    s ? (s << '}') : '{}'
+  end
+
+  alias inspect to_s
+
+  FETCH = Proc.new {|k| raise KeyError, 'key not found'}
+
+  # A single node in the doubly linked LRU list of nodes
+  Node = Struct.new :key, :value, :pred, :succ do
+    def unlink
+      pred.succ = succ if pred
+      succ.pred = pred if succ
+      self.succ = self.pred = nil
+      self
+    end
+
+    def insert_after(node)
+      raise 'Cannot insert after self' if equal? node
+      return self if node.succ.equal? self
+
+      unlink
+
+      self.succ = node.succ
+      self.pred = node
+
+      node.succ.pred = self if node.succ
+      node.succ = self
+
+      self
+    end
+  end
+
+  private
+  # iterate nodes
+  def each_node
+    n = @head.succ
+
+    until n.equal? @tail
+      succ = n.succ
+      yield n
+      n = succ
+    end
+
+    self
+  end
+
+  # move node to front
+  def front(node)
+    node.insert_after(@head)
+  end
+
+  # remove the node and invoke release_proc
+  # if set
+  def remove_node(node)
+    n = @h.delete(node.key)
+    n.unlink
+    release_proc and release_proc[n.key, n.value]
+    n
+  end
+
+  # remove the oldest node returning the node
+  def delete_oldest
+    n = @tail.pred
+    raise "Cannot delete from empty hash" if @head.equal? n
+    remove_node n
+  end
+
+  # Normalize the argument in order to be usable as max_size
+  # criterion is that n.to_i must be an Integer and it must
+  # be larger than zero.
+  def normalize_max(n)
+    n = n.to_i
+    raise ArgumentError, 'Invalid max_size: %p' % n unless Integer === n && n > 0
+    n
+  end
+end

data/spec/gff3_assemble2_spec.rb

@@ -0,0 +1,73 @@
+# RSpec for BioRuby-GFF3-Plugin. Run with something like:
+#
+#   ruby -I ../bioruby/lib/ ~/.gems/bin/spec spec/gff3_assemble2_spec.rb 
+#
+# Copyright (C) 2010 Pjotr Prins <pjotr.prins@thebird.nl>
+#
+$: << "../lib"
+
+require 'bio/db/gff/gffdb'
+
+include Bio::GFFbrowser
+
+FASTAFILE2="test/data/gff/MhA1_Contig125.fa"  
+GFF3FILE2="test/data/gff/MhA1_Contig125.gff3"
+
+PROTEINS = {
+  "cds:MhA1_Contig125.frz3.gene2" =>
+    "MNDLVNQFKSAALAVGQYLTPVLRESKFKETGVLTPEEFVAAGDHLVHLCPTWSWAKASDSNGQTTFLITKQSALVTQRCAQIMGYDEILKEKIIKDESAETGDEQNEWVDTHHFDFETNCAPKDFEEEENKVEDIKENNLNEEENCEEEEEGEPIDLDEYLSSGLLEEEDPARFVLQNKSLKETKDDSTSNNLLRTRRYDLHITYDKYYQVPRFWLVGYDENGSPLAVDKMKEDFSQEHADKTITLESHPHISGLTLATIHPCRHAPVMKRLIEQFQESGKELLVIDYLFVFLKFVQAVIPTVEYDYTRSIHF*",
+  "cds:MhA1_Contig125.frz3.gene3" =>
+"MERRKVSNTDPFEAAEGMLRWNSDIIKDKEIKQFKGLKKPLKLSENQNDEYDVDPFEAVTDWLPLNKNVDKT*",
+  "cds:MhA1_Contig125.frz3.gene4" =>
+    "MKSTKMSATEIVSYHLYSLHTLSSFCLTENPENIFIKDQNFQDFFLFCERVREQFNEAEELKTPLNTKISQTDSTNIQNKKDEPSISIGPCVNDLCPKGFECIENICFKSMEMPKTERVLSIGPCVNAKCPEGFSCYEDDRQCYAN*",
+  "cds:MhA1_Contig125.frz3.gene5" =>
+"MRLDIFLVIAFSLGVAVNCGVVKRSQNSYGDEAGAGGAAGAAPAAAAAPAGGEAAAPSGGETGGAAAPAEAAPAAAPAPEAAPAAAPAPEQAAPAVAQPAPAAAPSQASGYRKKRSQNSYGDEAGHAAGAAPAEAAAPAAGGEAAAPSGGETGGAAAPAETAPAAAPEAAPAAAPAPEQAAPAVAQPAPAAAPSQASGYRKKRSQNSYGDEAGAGGAAGAAPAAAAAPAGGEAAAPAAGGCTEGCAAGGESAAPAAAPAPEAAPAAAPAPEQAAPAVAQPAPAAAPSQASGYRKKRSQNSYGDEAGHAAGAAPAESAAPAAGGEAAAPSGGETGGAAAPAETAPAAAPEAAPAAAPEQAAPAVAQPAPAAAPSQASGY*",
+  "cds:MhA1_Contig125.frz3.gene6" =>
+"MDNAENEEKNDKENHEKPIKFEINNQKQFFKKEDEVKECEEESKNVNEFEEDQGTNEVSEVLRLFRRGNVWAFALQNLDLMRAYVILSCLAIAVVMLANFLRNSRFFDFCLK*",
+  "cds:MhA1_Contig125.frz3.gene7" =>
+"MLFCLLHPMDHNTGPLARKSSTLCSLLLLSIAALLVLAVPGQANSEEVGFGNHTKEKDGDEVTVNIDSVQAPDDLTYAVYEKRFKDVCEFVITKDDIELLYKGKGCTVELLTGENQDITFKTGVKDIGCVRNDCDKASLYSSVGEVEPGLSQSVTDGKTEFELRISGSEFNMNFEEDAPFNPQKNRCAPKQDHIVKPETWRIKNGELKDKHLLVFHLLPKTATREYTKEGKISKEQPPEEAPKCKLFIRFKRPYYEFLYVGPITTTVTTTTTTTTTPSSGLVGQGPTPKTGTHQGNTPKVQGKGSEKESDNTMMIVIIVIVVVVVVLVIGVVLIFILKNKGSKEDELQKVKQTTTKANKSSAVTL*",
+"cds:MhA1_Contig125.frz3.gene8" =>
+"MRQRESVILNKTENQTQIFEKLLNLYNSPKDVVNLRNNPEQLIQLGIDSKQFSAILEMMFGARRRNSLRGDYREARRFRNRREYSAWWDAGEVNNWRINSRHPSRHGTVEYWRCAFAVGRFFTCPSRIRITFGFGDRYVIVANARNHPHNHNRQNNAGDNNPNTVRRALPMEANERLTARTVHIGPRPSTSAPNQPTTKGQAAPPRASVSTTSANAAATPTTSASSTVQKGTAAPSTSAAPSTSAAPSTSAASRPLKPPGFATAATSATNSQQAAAKPASNQQPAPTATTSQTSASAPGTSSKPPPTTSPAPAATPAPATSQPGTSTVKSAPASTPTPLKPPAATEKQTSQPPSAAPGTTATIKPVLVTNIPGLPPGIPTSATGSGTINVSLTALDAFLAGHPRPASTSAPASSQTTPGPASQPSSAPVTQNKGKEEKKEDKKEEKKEGKKEEKKEGKKEEKRGPG*",
+"cds:MhA1_Contig125.frz3.gene9" =>
+"MHGATIGNRLRATRRSRDAQMMAAAESVARLSRRHSHQKAIRRVLPPPPALNSSRDSQPINPFCSDPSSIQPVIAKGVCVRSVGVFKSALPPSTPFPSTSTAPNIPSDNTFVPHLNNSTPLHNNHHRTLGGSENCLNYQQQYIGGSYSARSQQQHPPPPAPSSCCISPFKPLEILGNSNGTTDSSSGGCNSARAAMHRQFTGSSNGEEEFTVEELQEFAQAFKMFDKDGNGTMSIKELGVAMRTLGLNPTEDELLNMVNEYDVDGNGIDFSEFCKMMKEMNKETDQELIRLAFRVFDKDGNGYITAQEFRHFMTIDYEEFVNAVAPIVNDGAKEDAPFFEKEQPTSFGQPITSGPPLASGKAKHF*",
+"cds:MhA1_Contig125.frz3.gene21" =>
+"MDVKPPPSAPQDIKEAIKESNMSTWRPFLIGNRMRTTSEDSAESFDAYDKSFDAYDVGNKKERRLSITEQFFGSSMPGRLRSNSTTEYEGHEHEPTFKKVDLKQFMKHQRKILGDDEWQ*",
+"cds:MhA1_Contig125.frz3.gene22" =>
+"MAKALISGFVSSGFISKSNISICTRSEATAKSWRLQGFTSAYSKDVFYSEVKKPRAIILIAVKPQIFPSFINEVKANEWFYFGVPGILCISIMSGISLQHFDKEMKSVGFDGHSMRLMPNVNCAVSTGTLVLSADPETPQELVTLVSVLSSYVGKCIRVDEAHFNAASSISGCGPAFIALVIEALADGGVVAGLSRELANQLAADTVKGTGHLFMTKMASVSPTSDNPSPAQLKDQVCSPAGTTIEGVRELEKHGVRSAFIEAIQASTRRAFELSQ*" }
+
+describe GFFdb, "Assemble CDS (Contig125)" do
+  before :all do 
+    # gffdb = Bio::GFFbrowser::GFFdb.new(GFF3FILE2, :fasta_filename => FASTAFILE2,:cache_components => :cache_none, :cache_records => :cache_none)
+    gffdb = Bio::GFFbrowser::GFFdb.new(GFF3FILE2, :fasta_filename => FASTAFILE2)
+    @gff = gffdb.assembler
+    @gff.parse
+    @contigsequence = @gff.sequencelist["MhA1_Contig125"]
+    @componentlist = {}
+    @cdslist = {}
+    @gff.each_CDS do | id, reclist, component |
+      @componentlist[id] = component
+      @cdslist[id] = reclist
+    end
+  end
+
+  it "should have the single contig" do 
+    @gff.sequencelist.size.should == 1
+    @gff.sequencelist["MhA1_Contig125"].should_not == nil
+    @gff.sequencelist["MhA1_Contig125"].size.should == 53702
+  end
+  PROTEINS.each do | name, seq |
+    it "should translate gene #{name}" do
+      recs = @cdslist[name]
+      component = @componentlist[name]
+      cds0 = recs[0]
+      cds0.seqname.should == 'MhA1_Contig125'
+      # ntseq = @gff.assemble(@contigsequence,component.start,recs,:codonize=>true)
+      # p [name, ntseq]
+      aaseq = @gff.assembleAA(@contigsequence,component.start,recs)
+      aaseq.should == seq
+    end
+  end
+end
+
+
+

data/spec/gff3_assemble3_spec.rb

@@ -0,0 +1,62 @@
+# RSpec for BioRuby-GFF3-Plugin. Run with something like:
+#
+#   ruby -I ../bioruby/lib/ ~/.gems/bin/spec spec/gff3_assemble3_spec.rb 
+#
+# Copyright (C) 2010 Pjotr Prins <pjotr.prins@thebird.nl>
+#
+$: << "../lib"
+
+require 'bio/db/gff/gffdb'
+
+include Bio::GFFbrowser
+
+GFF3FILE3="test/data/gff/test-cds.gff3"
+
+describe GFFdb, "Assemble CDS (extra checks)" do
+  before :all do 
+    gffdb = Bio::GFFbrowser::GFFdb.new(GFF3FILE3)
+    @gff = gffdb.assembler
+    @gff.parse
+  end
+
+  it "should translate gene MhA1_Contig1040.frz3.gene29" do
+    @contigsequence = @gff.sequencelist["MhA1_Contig1040"]
+    @componentlist = {}
+    @cdslist = {}
+    @gff.each_CDS do | id, reclist, component |
+      @componentlist[id] = component
+      @cdslist[id] = reclist
+    end
+    name = "cds:MhA1_Contig1040.frz3.gene"
+    recs = @cdslist[name]
+    component = @componentlist[name]
+    p recs
+    ntseq = @gff.assemble(@contigsequence,component.start,recs,:raw=>true)
+    ntseq.should == "TTAATTAATTTGCCTAGAAAAACAAAGGCATAACATGCTTGCAGTCATCATACGGTAAGAGAGAAACCAACGATATGTTAATAATGTTGATGGGGGAATATCCTCATTAGAATTCTTTTTTGGGTGAATTGAAATTGCCATATTATTAGTATTATTAGAAAATATTAAATTTGTTGATAA"
+    ntseq = @gff.assemble(@contigsequence,component.start,recs,:codonize=>true)
+    ntseq.should == "TTATCAACAAATTTAATATTTTCTAATAATACTAATAATATGGCAATTTCAATTCACCCAAAAAAGAATTCTAATGAGGATATTCCCCCATCAACATTATTAACATATCGTTGGTTTCTCTCTTACCGTATGATGACTGCAAGCATGTTATGCCTTTGTTTTTCTAGGCAAATTAATTAA"
+    aaseq = @gff.assembleAA(@contigsequence,component.start,recs)
+    aaseq.should == "LSTNLIFSNNTNNMAISIHPKKNSNEDIPPSTLLTYRWFLSYRMMTASMLCLCFSRQIN*"
+  end
+  it "should translate gene MhA1_Contig2992.frz3.gene1" do
+    @contigsequence = @gff.sequencelist["MhA1_Contig2992"]
+    @componentlist = {}
+    @cdslist = {}
+    @gff.each_CDS do | id, reclist, component |
+      @componentlist[id] = component
+      @cdslist[id] = reclist
+    end
+    name = "cds:MhA1_Contig2992.frz3.gene1"
+    recs = @cdslist[name]
+    component = @componentlist[name]
+    # ntseq = @gff.assemble(@contigsequence,component.start,recs,:raw=>true)
+    # ntseq.should == ""
+    ntseq = @gff.assemble(@contigsequence,component.start,recs,:codonize=>true)
+    ntseq.should == "AAAATTAATAAAAAAATAAATGATAATTCTTTTAATATTCAATCTGATTCGAATGAAAATTTGTTTAATGATGGAATTAATTCTGAACAAAATGAAGACAATATAGCAACAAAAAAAGGCAACAAAAAATTCGGTAAAAATCAAAAAGAAGGAAATAAAGAGTTGGATATTCAAAGTGAAGGTTTTGATAATAATGAAATACCTTCAAAAGAAAGCAAAAAACAAATAAGTAATTTTGGGGATAATGAAAGTGAATATGAAAAAGAAGAGGATAATAGAAAAAAGAAAGGGAAAAAAGGAATGATAGAAAAGTATGAATTAGGAAGGAATAAAGGAAGGGATAAAAATGAAAGAAATAAGGCTTCTGAAAGGTTTGATGAGCAGAATCAAGACAGAAATAATCAACGTGATAGTTTTGATTCTGGCAATAATGATAAATCACAAAGAGGCTTAGATAGCGGCACATTAGATGGAACAAATAATTTAAAAAGATCGAATGATGATCAATTACCAGAATTTTTGAAAACGGCCAGTCTCTCAGAGCGTCAGAAATTTCTTCAACTTGAAGCAGAAAATGACAGGTCCAAGTCTTCTATACGAAGAGATAAACAGAATTGGGCTGATCAACAAGGGCAGAGAATTTCTGATCTTTATAAACAATTTCAACAATCTTTACAACAAAAAGAAAAACAATTTAAAAGTGAACGTCAACGAAATGTTCAAATTAAATTAAGCAGAAATGCACAGAATGTTGATAAAAGAATTCAGGATCTTCTGAATAATCCTGATATTGCTGAAAGAGCTTTAATTCTTCAAATTGAACAAATCCTCGGCGGTACAGACGATAGTATTCGTCAGGAATTACAAAGACAAATATCTGTTATTGGACCATTAGATGGAAATATACCGCCAAATCTTACATAG"
+    aaseq = @gff.assembleAA(@contigsequence,component.start,recs)
+    aaseq.should == "KINKKINDNSFNIQSDSNENLFNDGINSEQNEDNIATKKGNKKFGKNQKEGNKELDIQSEGFDNNEIPSKESKKQISNFGDNESEYEKEEDNRKKKGKKGMIEKYELGRNKGRDKNERNKASERFDEQNQDRNNQRDSFDSGNNDKSQRGLDSGTLDGTNNLKRSNDDQLPEFLKTASLSERQKFLQLEAENDRSKSSIRRDKQNWADQQGQRISDLYKQFQQSLQQKEKQFKSERQRNVQIKLSRNAQNVDKRIQDLLNNPDIAERALILQIEQILGGTDDSIRQELQRQISVIGPLDGNIPPNLT*"
+  end
+end
+
+
+

data/spec/gff3_assemble_spec.rb

@@ -0,0 +1,291 @@
+# RSpec for BioRuby-GFF3-Plugin. Run with something like:
+#
+#   ruby -I ../bioruby/lib/ ~/.gems/bin/spec spec/gff3_assemble_spec.rb 
+#
+# Copyright (C) 2010 Pjotr Prins <pjotr.prins@thebird.nl>
+#
+$: << "../lib"
+
+require 'bio/db/gff/gffdb'
+
+include Bio::GFFbrowser
+
+FASTAFILE="test/data/gff/MhA1_Contig1133.fa"  
+GFF3FILE="test/data/gff/MhA1_Contig1133.gff3"
+
+describe GFFdb, "Assemble CDS" do
+  before :all do 
+    gffdb = Bio::GFFbrowser::GFFdb.new(GFF3FILE, :fasta_filename => FASTAFILE)
+    @gff = gffdb.assembler
+    @gff.parse
+    @contigsequence = @gff.sequencelist["MhA1_Contig1133"]
+    @componentlist = {}
+    @cdslist = {}
+    @gff.each_CDS do | id, reclist, component |
+      @componentlist[id] = component
+      @cdslist[id] = reclist
+    end
+  end
+
+  it "should have the single contig" do 
+    @gff.sequencelist.size.should == 1
+    @gff.sequencelist["MhA1_Contig1133"].should_not == nil
+    @gff.sequencelist["MhA1_Contig1133"].size.should == 33905
+  end
+  it "should have a container component" do
+    component = @componentlist['cds:MhA1_Contig1133.frz3.gene4']
+    component.start.should == 7838
+    component.end.should == 8740
+  end
+  it "should have CDS 7838:7980" do
+    recs = @cdslist['cds:MhA1_Contig1133.frz3.gene4']
+    cds0 = recs[0]
+    cds0.start.should == 7838
+    cds0.end.should == 7980
+    cds0.frame.should == 0
+    cds0.seqname.should == 'MhA1_Contig1133'
+  end
+  it "should have CDS 8065:8308" do
+    recs = @cdslist['cds:MhA1_Contig1133.frz3.gene4']
+    cds1 = recs[1]
+    cds1.start.should == 8065
+    cds1.end.should == 8308
+    cds1.frame.should == 1
+    cds1.strand.should == '+'
+    cds1.seqname.should == 'MhA1_Contig1133'
+  end
+  # From Wormbase website http://www.wormbase.org/db/gb2/gbrowse/m_hapla/?name=MhA1_Contig1133%3A7838..8740
+  # >MhA1_Contig1133:7838..8740
+  # atgcgtcctttaacagatgaagaaactgaaaagtttttcaaaaaactttcaaattatatt
+  # ggtgacaatattaaacttttattggaaagagaagatggagaatatgtttttcgtttacat
+  # aaagacagagtttattattgcaggtttttttaaaattattttatatttaaattaggtctc
+  # aatctttataggggattttgtttttgttatttttttttggtttttag>tgaaaaattaatg
+  # cgacaagcagcatgtattggacgtaaacaattgggatcttttggaacttgtttgggtaaa
+  # ttcacaaaaggagggtctttctttcttcatataacatcattggattatttggcaccttat
+  # gctttagcaaaaatttggttaaaaccacaagctgaacaacaatttttatatggaaataat
+  # attgttaaatctggtgttggaagaatgagtgaagggattgaagaaaaacaagtaaatatt
+  # taattattttttttaaaatggattcctttacttctcaattaaatattaaaagcatatctg
+  # tagaagaggttatttatctttaaatcgaaatatacaggaataaataaaaatttaagaaat
+  # cataatttagaattctttttctggttatgttagattatttttaaatttttttgtaatttt
+  # tttttcgtaatttttttatgagcaaatcccttctctcttaaatattttaataaaaatcta
+  # attttataaattataattattttttagggtattattatttataatatgtcagatttacca
+  # ttgggttttggagtggctgcaaagggaacattatcttgtagaaaagtagatcctacagct
+  # ttagttgttttacatcaatcagatttgggtgaatatattcgaaatgaagagggattaatt
+
+  it "should translate CDS 7838:7980 (in frame 0, + strand)" do
+    recs = @cdslist['cds:MhA1_Contig1133.frz3.gene4']
+    component = @componentlist['cds:MhA1_Contig1133.frz3.gene4']
+    cds0 = recs[0]
+    cds0.seqname.should == 'MhA1_Contig1133'
+    seq = @gff.assemble(@contigsequence,component.start,[cds0])
+    seq.size.should == 143
+    seq.should == "ATGCGTCCTTTAACAGATGAAGAAACTGAAAAGTTTTTCAAAAAACTTTCAAATTATATTGGTGACAATATTAAACTTTTATTGGAAAGAGAAGATGGAGAATATGTTTTTCGTTTACATAAAGACAGAGTTTATTATTGCAG"
+    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds0])
+    aaseq.should == "MRPLTDEETEKFFKKLSNYIGDNIKLLLEREDGEYVFRLHKDRVYYC"
+  end
+  it "should translate CDS 8065:8308 (in frame 1, + strand)" do
+    recs = @cdslist['cds:MhA1_Contig1133.frz3.gene4']
+    component = @componentlist['cds:MhA1_Contig1133.frz3.gene4']
+    cds1 = recs[1]
+    seq = @gff.assemble(@contigsequence,component.start,[cds1], :phase => false)
+    seq.size.should == 244
+    seq.should == "TGAAAAATTAATGCGACAAGCAGCATGTATTGGACGTAAACAATTGGGATCTTTTGGAACTTGTTTGGGTAAATTCACAAAAGGAGGGTCTTTCTTTCTTCATATAACATCATTGGATTATTTGGCACCTTATGCTTTAGCAAAAATTTGGTTAAAACCACAAGCTGAACAACAATTTTTATATGGAAATAATATTGTTAAATCTGGTGTTGGAAGAATGAGTGAAGGGATTGAAGAAAAACAA"
+    seq = @gff.assemble(@contigsequence,component.start,[cds1])
+    seq.should == "GAAAAATTAATGCGACAAGCAGCATGTATTGGACGTAAACAATTGGGATCTTTTGGAACTTGTTTGGGTAAATTCACAAAAGGAGGGTCTTTCTTTCTTCATATAACATCATTGGATTATTTGGCACCTTATGCTTTAGCAAAAATTTGGTTAAAACCACAAGCTGAACAACAATTTTTATATGGAAATAATATTGTTAAATCTGGTGTTGGAAGAATGAGTGAAGGGATTGAAGAAAAACAA"
+    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds1])
+    # note it should handle the frame shift and direction!
+    aaseq.should == "EKLMRQAACIGRKQLGSFGTCLGKFTKGGSFFLHITSLDYLAPYALAKIWLKPQAEQQFLYGNNIVKSGVGRMSEGIEEKQ"
+  end
+  it "should translate CDS3 (in frame 0, + strand)" do
+    recs = @cdslist['cds:MhA1_Contig1133.frz3.gene4']
+    component = @componentlist['cds:MhA1_Contig1133.frz3.gene4']
+    cds3 = recs[2]
+    seq = @gff.assemble(@contigsequence,component.start,[cds3], :phase => false)
+    seq.size.should == 156
+    seq.should == "GGTATTATTATTTATAATATGTCAGATTTACCATTGGGTTTTGGAGTGGCTGCAAAGGGAACATTATCTTGTAGAAAAGTAGATCCTACAGCTTTAGTTGTTTTACATCAATCAGATTTGGGTGAATATATTCGAAATGAAGAGGGATTAATTTAA"
+    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds3])
+    # note it should handle the frame shift and direction!
+    aaseq.should == "GIIIYNMSDLPLGFGVAAKGTLSCRKVDPTALVVLHQSDLGEYIRNEEGLI*"
+  end
+  it "should assemble 3 CDSs for MhA1_Contig1133.frz3.gene4" do
+    recs = @cdslist['cds:MhA1_Contig1133.frz3.gene4']
+    component = @componentlist['cds:MhA1_Contig1133.frz3.gene4']
+    seq = @gff.assemble(@contigsequence,component.start,recs, :phase=>false)
+    seq.size.should == 543
+    seq.should == "ATGCGTCCTTTAACAGATGAAGAAACTGAAAAGTTTTTCAAAAAACTTTCAAATTATATTGGTGACAATATTAAACTTTTATTGGAAAGAGAAGATGGAGAATATGTTTTTCGTTTACATAAAGACAGAGTTTATTATTGCAGTGAAAAATTAATGCGACAAGCAGCATGTATTGGACGTAAACAATTGGGATCTTTTGGAACTTGTTTGGGTAAATTCACAAAAGGAGGGTCTTTCTTTCTTCATATAACATCATTGGATTATTTGGCACCTTATGCTTTAGCAAAAATTTGGTTAAAACCACAAGCTGAACAACAATTTTTATATGGAAATAATATTGTTAAATCTGGTGTTGGAAGAATGAGTGAAGGGATTGAAGAAAAACAAGGTATTATTATTTATAATATGTCAGATTTACCATTGGGTTTTGGAGTGGCTGCAAAGGGAACATTATCTTGTAGAAAAGTAGATCCTACAGCTTTAGTTGTTTTACATCAATCAGATTTGGGTGAATATATTCGAAATGAAGAGGGATTAATTTAA"
+    seq = @gff.assemble(@contigsequence,component.start,recs)
+    seq.size.should == 543
+    seq.should == "ATGCGTCCTTTAACAGATGAAGAAACTGAAAAGTTTTTCAAAAAACTTTCAAATTATATTGGTGACAATATTAAACTTTTATTGGAAAGAGAAGATGGAGAATATGTTTTTCGTTTACATAAAGACAGAGTTTATTATTGCAGTGAAAAATTAATGCGACAAGCAGCATGTATTGGACGTAAACAATTGGGATCTTTTGGAACTTGTTTGGGTAAATTCACAAAAGGAGGGTCTTTCTTTCTTCATATAACATCATTGGATTATTTGGCACCTTATGCTTTAGCAAAAATTTGGTTAAAACCACAAGCTGAACAACAATTTTTATATGGAAATAATATTGTTAAATCTGGTGTTGGAAGAATGAGTGAAGGGATTGAAGAAAAACAAGGTATTATTATTTATAATATGTCAGATTTACCATTGGGTTTTGGAGTGGCTGCAAAGGGAACATTATCTTGTAGAAAAGTAGATCCTACAGCTTTAGTTGTTTTACATCAATCAGATTTGGGTGAATATATTCGAAATGAAGAGGGATTAATTTAA"
+    aaseq = @gff.assembleAA(@contigsequence,component.start,recs)
+    aaseq.should == "MRPLTDEETEKFFKKLSNYIGDNIKLLLEREDGEYVFRLHKDRVYYCSEKLMRQAACIGRKQLGSFGTCLGKFTKGGSFFLHITSLDYLAPYALAKIWLKPQAEQQFLYGNNIVKSGVGRMSEGIEEKQGIIIYNMSDLPLGFGVAAKGTLSCRKVDPTALVVLHQSDLGEYIRNEEGLI*"
+  end
+  # > class=Sequence position=MhA1_Contig1133:27463..29904 (- strand); shown in frame 1!
+  # ATGGACCATC ATGCATTGGT GGAGGAATTA CCAGAAATTG AAAAATTAAC TCCTCAAGAA CGTATTGCAT TAGCTAGAGA
+  # ACGCCGTGCT GAACAACTTC GACAGAATGC TGCACGGGAG GCTCAATTGC CAATGCCTGC ACAGCGCCGG CCTCGTCTTC
+  # GATTTACACC AGATGTTGCT TTACTTGAGG CAACAGTTAG GGGTGATACC CAAGAAGGTT ATACATAAAG ATTATTGATT
+  # TTAAATGAAT TTATTTATTT TTTAGTTGAA AGACTTTTAA TGGAAGGTGT CAATGCTGAT TCACATAATG AGGATGGATT
+  # AACACCTTTA CATCAGGCAA AAACCAAATT AATTTTTTTA AATTTATTTT TAGTGTGCCA TTGACAATAA TGAAAGAATT
+  # GTTCGTCTTC TGCTTAGGTA CGGAGCTTGT GTTAATGCCA AAGACACTGA ACTTTGGACA CCATTGCACG CAGCTGCATG
+  # TTGTGCTTAT ATTGATATTG TTCGATTGCT TATTGCACAG TTAGTTTTTT TTTAATTTTT TTTTTAAATA AATTTCTTAA
+  # GTTTTACAGA AATATTTATT TTAAACAAAC GGGACTTCCT TTTAAATTTT TTGTATTTTT AATCTTTACG TATTTTCATT
+  # TAATAATTAA TTCGTCTTCT AAAAGTTCGT AAGTTTTGTG GTTTAGTTTA ATGGGTAAAC ATCCAGTTTT TAGGTCATCG
+  # ATTTTTATTT TTGCGTCATA TTTTATCGAA AACTTCTTTC ATATTAAAAA TTTCTTTTTA AGCAACGCAG ATTTACTAGC
+  # AGTAAATGCA GATGGTAATA TGCCTTATGA TATTTGTGAT GATGAACAAA CCCTTGACCT TATTGAATCT GAAATGGCTG
+  # CTAGAGGAAT TACACAAGAA ATGATTGATG AAAGAAGACA ACAACCAGAA AGGGAAATGT TAAATGATAT GAAAATTTTA
+  # CATCAAAGAG GATTACCTTT AGATCAAAGA AATTCTGTTG ATAAATCTAC TTTTGTAAGT TTTTCTGGAG AAAGGGAAAT
+  # TTATGTAAAG ATTATTATGA AAGGATTATT ACAGTTTTAT TCCTTTTTAG TTACATATAG CAGCAGCTAA TGGTTATTAT
+  # GATGTTGCTG CTTTCCTTCT TCGTTGTAAT GTTTCTCCAG CATTGAGAGA TATAGATTTG TGGCAACCAA TTCATGCAGC
+  # TGCTTCTTGG AATCAACCAG ACTTAATCGA GCTTTTATGC GAATATGGGG CTGATATAAA TGCAAAAACT GGAGCTGGGG
+  # AAAGCCCTTT AGGTTTATTT TATTGAATCT TATAATTTAT AAATATTTGC TATTAAGTAT GAGGGGAGAG GAACTAACAA
+  # TAAGGAATTA AATTTCTCAA TATCAGGATT TTTCGGTTCA CACCCATTTT CTTAAGACCT TTAATTTTTC TCAAAATATG
+  # TATGTGACCA CGTCGGGAGG CTTTTTTATT TTTACATGGC TATTTTAAGA AAGGCTAGAA TTTTGACATA CTTTTAACTT
+  # ATCGCCTTCC TAACTATTTT CTGTCTATAT ATTTTTTTAA ATTAAGAATT AACTGAAGAT GAACCAACCC AACAAGTAAT
+  # TAGAACAATC GCTCAGACAG AAGCAAGGAG ACGGCGTGGT CCAGGTGGTG GTTACTTTGG TGTTCGTGAT TCTCGACGAC
+  # AAAGCCGAAA GTAATTTTAA ATTTATATTT TCTTTTCATC TTTTTATCTA GAAGAAAAAA GTTTGAATCT CCTCAACAAC
+  # CACCTTCAAC ATTAGAAAAT CCTTTCTCAG CTAGAGGTGC AATTAGACGA CAATCATTGC GAGATCGTAG TGGAATGTCA
+  # TTAGCTCGTT TGGAAGCACA AAGAGAGGGT TCTGACCTTA TTAGAAGTTA TAATAGTAAA GAAGACCTTT CTTCTAATAC
+  # AGCGGTTTGT TTTTTAAAAT TGTAATTTTT TCTTAATTTT TAGGATGATT CTTTAAATGT TGGAAGTTCT TCATATCTCA
+  # ACAATCCAAC AGCCTCGGCT AGTGCTTCCT CTTCAGCATT ACACGGAACT CCACATCAAC AACAACGTCG TGAATCTCCA
+  # CCTAAACGTG CATTAATGGC TAGAAGTGCT TCTCATCAAA AACAAAAACA ACAAATGTCT CCAGATGAAT GGCTGAAAAA
+  # ATTAGAAGCA GATTCTGCAG GTTTTCGAGA TAATGATGGA GAAGATGGTG AATTACAATC TGAACTTAAA GGAGGACAAA
+  # GAATGAAGAG TGGTGGTGGT GGAGGAGCGA GAGGTCAGCA AGGTGAATTA AAATATTTTT TTTGAATTTT ATATTTATTT
+  # TTCGTTTAAT AGAAATGAAT GGTGGTCCAA CAGCAACATT TGGTGGAGCT TCAAAACAAC AATTAGCAAT GGGCTCTGGA
+  # CCCAATAGAC GGCGCAAACA AGGATGTTGC TCTGTTTTGT GA
+  it "should assemble a reverse CDS in MhA1_Contig1133.frz3.gene11" do
+    recs = @cdslist['cds:MhA1_Contig1133.frz3.gene11']
+    recs.size.should == 8
+    component = @componentlist['cds:MhA1_Contig1133.frz3.gene11']
+    # 193 bp from MhA1_Contig1133:27,981..28,173
+    # >MhA1_Contig1133:27981..28173
+    # cgctgtattagaagaaaggtcttctttactattataacttctaataaggtcagaaccctc
+    # tctttgtgcttccaaacgagctaatgacattccactacgatctcgcaatgattgtcgtct
+    # aattgcacctctagctgagaaaggattttctaatgttgaaggtggttgttgaggagattc
+    # aaacttttttctt
+    cds1 = recs[5]
+    cds1.start.should == 27981
+    cds1.frame.should == 1
+    cds1.strand.should == '-'
+    seq = @gff.assemble(@contigsequence,component.start,[cds1],:phase=>true,:reverse=>true)
+    seq.should == "TCTTTTTTCAAACTTAGAGGAGTTGTTGGTGGAAGTTGTAATCTTTTAGGAAAGAGTCGATCTCCACGTTAATCTGCTGTTAGTAACGCTCTAGCATCACCTTACAGTAATCGAGCAAACCTTCGTGTTTCTCTCCCAAGACTGGAATAATCTTCAATATTATCATTTCTTCTGGAAAGAAGATTATGTCGC"
+    seq.size.should == 192
+    seq = @gff.assemble(@contigsequence,component.start,[cds1],:phase=>true,:reverse=>true,:complement=>true)
+    seq.should == "AGAAAAAAGTTTGAATCTCCTCAACAACCACCTTCAACATTAGAAAATCCTTTCTCAGCTAGAGGTGCAATTAGACGACAATCATTGCGAGATCGTAGTGGAATGTCATTAGCTCGTTTGGAAGCACAAAGAGAGGGTTCTGACCTTATTAGAAGTTATAATAGTAAAGAAGACCTTTCTTCTAATACAGCG"
+    seq.size.should == 192
+    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds1])
+    # note it should handle the frame shift and direction!
+    # >EMBOSS_001_4
+    # RKKFESPQQPPSTLENPFSARGAIRRQSLRDRSGMSLARLEAQREGSDLIRSYNSKEDLSSNTA
+    aaseq.should == "RKKFESPQQPPSTLENPFSARGAIRRQSLRDRSGMSLARLEAQREGSDLIRSYNSKEDLSSNTA"
+  end
+  it "should take the 6th CDS in MhA1_Contig1133.frz3.gene11 (which is 3rd on DNA)" do
+    # >MhA1_Contig1133:27981..28173
+    # cgctgtattagaagaaaggtcttctttactattataacttctaataaggtcagaaccctc
+    # tctttgtgcttccaaacgagctaatgacattccactacgatctcgcaatgattgtcgtct
+    # aattgcacctctagctgagaaaggattttctaatgttgaaggtggttgttgaggagattc
+    # aaacttttttctt
+    recs = @cdslist['cds:MhA1_Contig1133.frz3.gene11']
+    component = @componentlist['cds:MhA1_Contig1133.frz3.gene11']
+    cds2 = recs[5].clone
+    # p cds2
+    cds2.start.should == 27981
+    cds2.frame.should == 1
+    cds2.strand.should == '-'
+    seq = @gff.assemble(@contigsequence,component.start,[cds2],:complement=>true)
+    seq.should == "GCGACATAATCTTCTTTCCAGAAGAAATGATAATATTGAAGATTATTCCAGTCTTGGGAGAGAAACACGAAGGTTTGCTCGATTACTGTAAGGTGATGCTAGAGCGTTACTAACAGCAGATTAACGTGGAGATCGACTCTTTCCTAAAAGATTACAACTTCCACCAACAACTCCTCTAAGTTTGAAAAAAGAA"
+    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds2])
+    # note it should handle the frame shift and direction!
+    # >27981..28173_4 RKKFESPQQPPSTLENPFSARGAIRRQSLRDRSGMSLARLEAQREGSDLIRSYNSKEDLSSNTA
+    aaseq.should == "RKKFESPQQPPSTLENPFSARGAIRRQSLRDRSGMSLARLEAQREGSDLIRSYNSKEDLSSNTA"
+  end
+  it "should assemble the 1st reverse CDS in MhA1_Contig1133.frz3.gene11" do
+    recs = @cdslist['cds:MhA1_Contig1133.frz3.gene11']
+    component = @componentlist['cds:MhA1_Contig1133.frz3.gene11']
+    cds1 = recs[0].clone
+    cds1.start.should == 29710
+    cds1.frame.should == 0
+    cds1.strand.should == '-'
+    seq = @gff.assemble(@contigsequence,component.start,[cds1],:raw=>true)
+    seq.size.should == 195
+    seq.should == "TGTTGCCTCAAGTAAAGCAACATCTGGTGTAAATCGAAGACGAGGCCGGCGCTGTGCAGGCATTGGCAATTGAGCCTCCCGTGCAGCATTCTGTCGAAGTTGTTCAGCACGGCGTTCTCTAGCTAATGCAATACGTTCTTGAGGAGTTAATTTTTCAATTTCTGGTAATTCCTCCACCAATGCATGATGGTCCAT"
+    seq = @gff.assemble(@contigsequence,component.start,[cds1],:codonize=>true)
+    seq.should == "ATGGACCATCATGCATTGGTGGAGGAATTACCAGAAATTGAAAAATTAACTCCTCAAGAACGTATTGCATTAGCTAGAGAACGCCGTGCTGAACAACTTCGACAGAATGCTGCACGGGAGGCTCAATTGCCAATGCCTGCACAGCGCCGGCCTCGTCTTCGATTTACACCAGATGTTGCTTTACTTGAGGCAACA"
+    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds1])
+    aaseq.should == "MDHHALVEELPEIEKLTPQERIALARERRAEQLRQNAAREAQLPMPAQRRPRLRFTPDVALLEAT"
+  end
+  it "should assemble the 3rd reverse CDS in MhA1_Contig1133.frz3.gene11" do
+    recs = @cdslist['cds:MhA1_Contig1133.frz3.gene11']
+    component = @componentlist['cds:MhA1_Contig1133.frz3.gene11']
+    cds2 = recs[2].clone
+    # CAACGCAG ATTTACTAGC AGTAAATGCA GATGGTAATA TGCCTTATGA TATTTGTGAT GATGAACAAA CCCTTGACCT TATTGAATCT GAAATGGCTG CTAGAGGAAT TACACAAGAA ATGATTGATG AAAGAAGACA ACAACCAGAA AGGGAAATGT TAAATGATAT GAAAATTTTA CATCAAAGAG GATTACCTTT AGATCAAAGA AATTCTGTTG ATAAATCTAC TTTTGTAAGT TTTTCTGGAG AAAGGGAAAT TTAT
+    # p cds2
+    cds2.frame.should == 1
+    cds2.strand.should == '-'
+    seq = @gff.assemble(@contigsequence,component.start,[cds2], :raw=>true)
+    seq.should == "ATAAATTTCCCTTTCTCCAGAAAAACTTACAAAAGTAGATTTATCAACAGAATTTCTTTGATCTAAAGGTAATCCTCTTTGATGTAAAATTTTCATATCATTTAACATTTCCCTTTCTGGTTGTTGTCTTCTTTCATCAATCATTTCTTGTGTAATTCCTCTAGCAGCCATTTCAGATTCAATAAGGTCAAGGGTTTGTTCATCATCACAAATATCATAAGGCATATTACCATCTGCATTTACTGCTAGTAAATCTGCGTTG"
+    seq = @gff.assemble(@contigsequence,component.start,[cds2], :codonize=>true)
+    seq.should == "AACGCAGATTTACTAGCAGTAAATGCAGATGGTAATATGCCTTATGATATTTGTGATGATGAACAAACCCTTGACCTTATTGAATCTGAAATGGCTGCTAGAGGAATTACACAAGAAATGATTGATGAAAGAAGACAACAACCAGAAAGGGAAATGTTAAATGATATGAAAATTTTACATCAAAGAGGATTACCTTTAGATCAAAGAAATTCTGTTGATAAATCTACTTTTGTAAGTTTTTCTGGAGAAAGGGAAATTTAT"
+    # cds1.frame = 1
+    aaseq = @gff.assembleAA(@contigsequence,component.start,[cds2])
+    # note it should handle the frame shift and direction!
+    aaseq.should == "NADLLAVNADGNMPYDICDDEQTLDLIESEMAARGITQEMIDERRQQPEREMLNDMKILHQRGLPLDQRNSVDKSTFVSFSGEREIY"
+  end
+  it "should assemble the protein sequence for MhA1_Contig1133.frz3.gene11" do
+    recs = @cdslist['cds:MhA1_Contig1133.frz3.gene11']
+    component = @componentlist['cds:MhA1_Contig1133.frz3.gene11']
+    seq = @gff.assemble(@contigsequence,component.start,recs, :phase=>true, :reverse=>true, :complement=>true)
+    seq.should == "ATGGACCATCATGCATTGGTGGAGGAATTACCAGAAATTGAAAAATTAACTCCTCAAGAACGTATTGCATTAGCTAGAGAACGCCGTGCTGAACAACTTCGACAGAATGCTGCACGGGAGGCTCAATTGCCAATGCCTGCACAGCGCCGGCCTCGTCTTCGATTTACACCAGATGTTGCTTTACTTGAGGCAACATGTGCCATTGACAATAATGAAAGAATTGTTCGTCTTCTGCTTAGGTACGGAGCTTGTGTTAATGCCAAAGACACTGAACTTTGGACACCATTGCACGCAGCTGCATGTTGTGCTTATATTGATATTGTTCGATTGCTTATTGCACACAACGCAGATTTACTAGCAGTAAATGCAGATGGTAATATGCCTTATGATATTTGTGATGATGAACAAACCCTTGACCTTATTGAATCTGAAATGGCTGCTAGAGGAATTACACAAGAAATGATTGATGAAAGAAGACAACAACCAGAAAGGGAAATGTTAAATGATATGAAAATTTTACATCAAAGAGGATTACCTTTAGATCAAAGAAATTCTGTTGATAAATCTACTTTTGTAAGTTTTTCTGGAGAAAGGGAAATTTATTTACATATAGCAGCAGCTAATGGTTATTATGATGTTGCTGCTTTCCTTCTTCGTTGTAATGTTTCTCCAGCATTGAGAGATATAGATTTGTGGCAACCAATTCATGCAGCTGCTTCTTGGAATCAACCAGACTTAATCGAGCTTTTATGCGAATATGGGGCTGATATAAATGCAAAAACTGGAGCTGGGGAAAGCCCTTTAGAATTAACTGAAGATGAACCAACCCAACAAGTAATTAGAACAATCGCTCAGACAGAAGCAAGGAGACGGCGTGGTCCAGGTGGTGGTTACTTTGGTGTTCGTGATTCTCGACGACAAAGCCGAAAAAGAAAAAAGTTTGAATCTCCTCAACAACCACCTTCAACATTAGAAAATCCTTTCTCAGCTAGAGGTGCAATTAGACGACAATCATTGCGAGATCGTAGTGGAATGTCATTAGCTCGTTTGGAAGCACAAAGAGAGGGTTCTGACCTTATTAGAAGTTATAATAGTAAAGAAGACCTTTCTTCTAATACAGCGGATGATTCTTTAAATGTTGGAAGTTCTTCATATCTCAACAATCCAACAGCCTCGGCTAGTGCTTCCTCTTCAGCATTACACGGAACTCCACATCAACAACAACGTCGTGAATCTCCACCTAAACGTGCATTAATGGCTAGAAGTGCTTCTCATCAAAAACAAAAACAACAAATGTCTCCAGATGAATGGCTGAAAAAATTAGAAGCAGATTCTGCAGGTTTTCGAGATAATGATGGAGAAGATGGTGAATTACAATCTGAACTTAAAGGAGGACAAAGAATGAAGAGTGGTGGTGGTGGAGGAGCGAGAGGTCAGCAAGAAATGAATGGTGGTCCAACAGCAACATTTGGTGGAGCTTCAAAACAACAATTAGCAATGGGCTCTGGACCCAATAGACGGCGCAAACAAGGATGTTGCTCTGTTTTGTGA"
+    aaseq = @gff.assembleAA(@contigsequence,component.start,recs)
+    aaseq.should == "MDHHALVEELPEIEKLTPQERIALARERRAEQLRQNAAREAQLPMPAQRRPRLRFTPDVALLEATCAIDNNERIVRLLLRYGACVNAKDTELWTPLHAAACCAYIDIVRLLIAHNADLLAVNADGNMPYDICDDEQTLDLIESEMAARGITQEMIDERRQQPEREMLNDMKILHQRGLPLDQRNSVDKSTFVSFSGEREIYLHIAAANGYYDVAAFLLRCNVSPALRDIDLWQPIHAAASWNQPDLIELLCEYGADINAKTGAGESPLELTEDEPTQQVIRTIAQTEARRRRGPGGGYFGVRDSRRQSRKRKKFESPQQPPSTLENPFSARGAIRRQSLRDRSGMSLARLEAQREGSDLIRSYNSKEDLSSNTADDSLNVGSSSYLNNPTASASASSSALHGTPHQQQRRESPPKRALMARSASHQKQKQQMSPDEWLKKLEADSAGFRDNDGEDGELQSELKGGQRMKSGGGGGARGQQEMNGGPTATFGGASKQQLAMGSGPNRRRKQGCCSVL*"
+    # >EMBOSS_001_1
+    # MDHHALVEELPEIEKLTPQERIALARERRAEQLRQNAAREAQLPMPAQRRPRLRFTPDVA
+    # LLEATCAIDNNERIVRLLLRYGACVNAKDTELWTPLHAAACCAYIDIVRLLIAHNADLLA
+    # VNADGNMPYDICDDEQTLDLIESEMAARGITQEMIDERRQQPEREMLNDMKILHQRGLPL
+    # DQRNSVDKSTFVSFSGEREIYLHIAAANGYYDVAAFLLRCNVSPALRDIDLWQPIHAA...
+
+  end
+  it "should assemble exons into"
+  it "should assemble the gene into" 
+  #   >MhA1_Contig1133:27463..29904
+  # tcacaaaacagagcaacatccttgtttgcgccgtctattgggtccagagcccattgctaa
+  # ttgttgttttgaagctccaccaaatgttgctgttggaccaccattcatttctattaaacg
+  # aaaaataaatataaaattcaaaaaaaatattttaattcaccttgctgacctctcgctcct
+  # ccaccaccaccactcttcattctttgtcctcctttaagttcagattgtaattcaccatct
+  # tctccatcattatctcgaaaacctgcagaatctgcttctaattttttcagccattcatct
+  # ggagacatttgttgtttttgtttttgatgagaagcacttctagccattaatgcacgttta
+  # ggtggagattcacgacgttgttgttgatgtggagttccgtgtaatgctgaagaggaagca
+  # ctagccgaggctgttggattgttgagatatgaagaacttccaacatttaaagaatcatcc
+  # taaaaattaagaaaaaattacaattttaaaaaacaaaccgctgtattagaagaaaggtct
+  # tctttactattataacttctaataaggtcagaaccctctctttgtgcttccaaacgagct
+  # aatgacattccactacgatctcgcaatgattgtcgtctaattgcacctctagctgagaaa
+  # ggattttctaatgttgaaggtggttgttgaggagattcaaacttttttcttctagataaa
+  # aagatgaaaagaaaatataaatttaaaattactttcggctttgtcgtcgagaatcacgaa
+  # caccaaagtaaccaccacctggaccacgccgtctccttgcttctgtctgagcgattgttc
+  # taattacttgttgggttggttcatcttcagttaattcttaatttaaaaaaatatatagac
+  # agaaaatagttaggaaggcgataagttaaaagtatgtcaaaattctagcctttcttaaaa
+  # tagccatgtaaaaataaaaaagcctcccgacgtggtcacatacatattttgagaaaaatt
+  # aaaggtcttaagaaaatgggtgtgaaccgaaaaatcctgatattgagaaatttaattcct
+  # tattgttagttcctctcccctcatacttaatagcaaatatttataaattataagattcaa
+  # taaaataaacctaaagggctttccccagctccagtttttgcatttatatcagccccatat
+  # tcgcataaaagctcgattaagtctggttgattccaagaagcagctgcatgaattggttgc
+  # cacaaatctatatctctcaatgctggagaaacattacaacgaagaaggaaagcagcaaca
+  # tcataataaccattagctgctgctatatgtaactaaaaaggaataaaactgtaataatcc
+  # tttcataataatctttacataaatttccctttctccagaaaaacttacaaaagtagattt
+  # atcaacagaatttctttgatctaaaggtaatcctctttgatgtaaaattttcatatcatt
+  # taacatttccctttctggttgttgtcttctttcatcaatcatttcttgtgtaattcctct
+  # agcagccatttcagattcaataaggtcaagggtttgttcatcatcacaaatatcataagg
+  # catattaccatctgcatttactgctagtaaatctgcgttgcttaaaaagaaatttttaat
+  # atgaaagaagttttcgataaaatatgacgcaaaaataaaaatcgatgacctaaaaactgg
+  # atgtttacccattaaactaaaccacaaaacttacgaacttttagaagacgaattaattat
+  # taaatgaaaatacgtaaagattaaaaatacaaaaaatttaaaaggaagtcccgtttgttt
+  # aaaataaatatttctgtaaaacttaagaaatttatttaaaaaaaaaattaaaaaaaaact
+  # aactgtgcaataagcaatcgaacaatatcaatataagcacaacatgcagctgcgtgcaat
+  # ggtgtccaaagttcagtgtctttggcattaacacaagctccgtacctaagcagaagacga
+  # acaattctttcattattgtcaatggcacactaaaaataaatttaaaaaaattaatttggt
+  # ttttgcctgatgtaaaggtgttaatccatcctcattatgtgaatcagcattgacaccttc
+  # cattaaaagtctttcaactaaaaaataaataaattcatttaaaatcaataatctttatgt
+  # ataaccttcttgggtatcacccctaactgttgcctcaagtaaagcaacatctggtgtaaa
+  # tcgaagacgaggccggcgctgtgcaggcattggcaattgagcctcccgtgcagcattctg
+  # tcgaagttgttcagcacggcgttctctagctaatgcaatacgttcttgaggagttaattt
+  # ttcaatttctggtaattcctccaccaatgcatgatggtccat
+end
+