# 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-gff3'

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