mspire 0.2.4 → 0.3.0

data/specs/transmem/toppred_spec.rb

@@ -0,0 +1,297 @@
+require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
+
+# contains shared behavior that we need.
+require File.expand_path( File.dirname(__FILE__) + '/../transmem_spec_shared' )
+
+require 'transmem/toppred'
+
+describe TopPred::Index do
+  before(:all) do
+    @toppred_file = Tfiles + '/toppred.small.out'
+    @obj = TopPred::Index.new(@toppred_file)
+    @test_hash = {"YAL001C"=>0, "YAL011W"=>0, "YAL009W"=>2, "YAL010C"=>1, "YAL008W"=>3, "YAL007C"=>2, "YAL004W"=>0, "YAL005C"=>1, "YAL003W"=>0, "YAL002W"=>3, "YAL013W"=>0, "YAL014C"=>1, "YAL012W"=>1}
+    @ref_to_key= { 'gi|16127905|ref|NP_414542.1| thr operon leader peptide [Escherichia coli K12]' => 'gi_16127905_ref_NP_414542_1_',
+      'SWN:PWP1_HUMAN PERIODIC TRYPTOPHAN PROTEIN 1 HOMOLOG' => 'SWN_PWP1_HUMAN',
+      'MY:B|/-"[super]"duper!@#$%^&*(wil) and other stuff' => 'MY_B_____super__duper_________wil_' }
+  end
+  it_should_behave_like 'a transmem index'
+end
+
+describe "a toppred parser", :shared => true do
+  it 'parses a toppred file into a hash structure' do
+    @file_to_hash.should exist
+    hash = @class.default_index(@file_to_hash)
+    hash.should == @structure_to_create
+  end
+end
+
+describe "TopPred parsing a text file" do
+  before(:all) do
+    @class = TopPred
+    @file_to_hash = Tfiles + '/toppred.small.out'
+    @structure_to_create = YAML.load(TopPredSupportingFile::MY_YAML1)
+    @structure_to_create.each {|id,hash| string_to_symbol(hash) }
+  end
+  it_should_behave_like 'a toppred parser'
+end
+
+describe "TopPred parsing an xml file" do
+  before(:all) do
+    @class = TopPred
+    @file_to_hash = Tfiles + '/toppred.xml.out'
+    @structure_to_create = YAML.load(TopPredSupportingFile::MY_YAML2)
+    @structure_to_create.each {|id,hash| string_to_symbol(hash) }
+  end
+  it_should_behave_like 'a toppred parser'
+end
+
+describe TopPred::Index do
+  before(:all) do
+    toppred_file = Tfiles + '/toppred.xml.out'
+    @obj = TopPred::Index.new(toppred_file)
+    @tm_test = {
+      :mykey => 'SWN_K1CL_HUMAN',
+      :seqs => %w(GFG VGSGYGGSAFGFG GGGSL),
+      :exps => 
+      {
+        :number => [2.0, 7.0, 3.0],
+        :fraction => [2.0/3, 7.0/13, 3.0/5 ],
+      }
+    }
+  end
+  it_should_behave_like "a calculator of transmembrane overlap"
+end
+
+
+module TopPredSupportingFile
+  MY_YAML1 = <<END
+--- 
+YAL011W: 
+  aaseq: MPAVLRTRSKESSIEQKPASRTRTRSRRGKRGRDDDDDDDDEESDDAYDEVGNDYDEYASRAKLATNRPFEIVAGLPASVELPNYNSSLTHPQSIKNSGVLYDSLVSSRRTWVQGEMFELYWRRPKKIVSESTPAATESPTSGTIPLIRDKMQKMCDCVMSGGPHTFKVRLFILKNDKIEQKWQDEQELKKKEKELKRKNDAEAKRLRMEERKRQQMQKKIAKEQKLQLQKENKAKQKLEQEALKLKRKEEMKKLKEQNKNKQGSPSSSMHDPRMIMNLNLMAQEDPKLNTLMETVAKGLANNSQLEEFKKFIEIAKKRSLEENPVNKRPSVTTTRPAPPSKAKDVAEDHRLNSITLVKSSKTAATEPEPKKADDENAEKQQSKEAKTTAESTQVDVKKEEEDVKEKGVKSEDTQKKEDNQVVPKRKRRKNAIKEDKDMQLTAFQQKYVQGAEIILEYLEFTHSRYYLPKKSVVEFLEDTDEIIISWIVIHNSKEIEKFKTKKIKAKLKADQKLNKEDAKPGSDVEKEVSFNPLFEADCPTPLYTPMTMKLSGIHKRFNQIIRNSVSPMEEVVKEMEKILQIGTRLSGYNLWYQLDGYDDEALSESLRFELNEWEHAMRSRRHKR
+  num_found: 0
+YAL001C: 
+  aaseq: MVLTIYPDELVQIVSDKIASNKGKITLNQLWDISGKYFDLSDKKVKQFVLSCVILKKDIEVYCDGAITTKNVTDIIGDANHSYSVGITEDSLWTLLTGYTKKESTIGNSAFELLLEVAKSGEKGINTMDLAQVTGQDPRSVTGRIKKINHLLTSSQLIYKGHVVKQLKLKKFSHDGVDSNPYINIRDHLATIVEVVKRSKNGIRQIIDLKRELKFDKEKRLSKAFIAAIAWLDEKEYLKKVLVVSPKNPAIKIRCVKYVKDIPDSKGSPSFEYDSNSADEDSVSDSKAAFEDEDLVEGLDNFNATDLLQNQGLVMEEKEDAVKNEVLLNRFYPLQNQTYDIADKSGLKGISTMDVVNRITGKEFQRAFTKSSEYYLESVDKQKENTGGYRLFRIYDFEGKKKFFRLFTAQNFQKLTNAEDEISVPKGFDELGKSRTDLKTLNEDNFVALNNTVRFTTDSDGQDIFFWHGELKIPPNSKKTPNKNKRKRQVKNSTNASVAGNISNPKRIKLEQHVSTAQEPKSAEDSPSSNGGTVVKGKVVNFGGFSARSLRSLQRQRAILKVMNTIGGVAYLREQFYESVSKYMGSTTTLDKKTVRGDVDLMVESEKLGARTEPVSGRKIIFLPTVGEDAIQRYILKEKDSKKATFTDVIHDTEIYFFDQTEKNRFHRGKKSVERIRKFQNRQKNAKIKASDDAISKKSTSVNVSDGKIKRRDKKVSAGRTTVVVENTKEDKTVYHAGTKDGVQALIRAVVVTKSIKNEIMWDKITKLFPNNSLDNLKKKWTARRVRMGHSGWRAYVDKWKKMLVLAIKSEKISLRDVEELDLIKLLDIWTSFDEKEIKRPLFLYKNYEENRKKFTLVRDDTLTHSGNDLAMSSMIQREISSLKKTYTRKISASTKDLSKSQSDDYIRTVIRSILIESPSTTRNEIEALKNVGNESIDNVIMDMAKEKQIYLHGSKLECTDTLPDILENRGNYKDFGVAFQYRCKVNELLEAGNAIVINQEPSDISSWVLIDLISGELLNMDVIPMVRNVRPLTYTSRRFEIRTLTPPLIIYANSQTKLNTARKSAVKVPLGKPFSRLWVNGSGSIRPNIWKQVVTMVVNEIIFHPGITLSRLQSRCREVLSLHEISEICKWLLERQVLITTDFDGYWVNHNWYSIYEST
+  num_found: 0
+YAL010C: 
+  num_putative_transmembrane_segments: 1
+  aaseq: MLPYMDQVLRAFYQSTHWSTQNSYEDITATSRTLLDFRIPSAIHLQISNKSTPNTFNSLDFSTRSRINGSLSYLYSDAQQLEKFMRNSTDIPLQDATETYRQLQPNLNFSVSSANTLSSDNTTVDNDKKLLHDSKFVKKSLYYGRMYYPSSDLEAMIIKRLSPQTQFMLKGVSSFKESLNVLTCYFQRDSHRNLQEWIFSTSDLLCGYRVLHNFLTTPSKFNTSLYNNSSLSLGAEFWLGLVSLSPGCSTTLRYYTHSTNTGRPLTLTLSWQPLFGHISSTYSAKTGTNSTFCAKYDFNLYSIESNLSFGCEFWQKKHHLLETNKNNNDKLEPISDELVDINPNSRATKLLHENVPDLNSAVNDIPSTLDIPVHKQKLLNDLTYAFSSSLRKIDEERSTIEKFDNKINSSIFTSVWKLSTSLRDKTLKLLWEGKWRGFLISAGTELVFTRGFQESLSDDEKNDNAISISATDTENGNIPVFPAKFGIQFQYST
+  best_structure_probability: 1.0
+  transmembrane_segments: 
+  - aaseq: SLGAEFWLGLVSLSPGCSTTL
+    stop: 252
+    start: 232
+    probability: 1.0
+  num_certain_transmembrane_segments: 1
+  num_found: 2
+YAL009W: 
+  num_putative_transmembrane_segments: 0
+  aaseq: MEPESIGDVGNHAQDDSASIVSGPRRRSTSKTSSAKNIRNSSNISPASMIFRNLLILEDDLRRQAHEQKILKWQFTLFLASMAGVGAFTFYELYFTSDYVKGLHRVILQFTLSFISITVVLFHISGQYRRTIVIPRRFFTSTNKGIRQFNVKLVKVQSTWDEKYTDSVRFVSRTIAYCNIYCLKKFLWLKDDNAIVKFWKSVTIQSQPRIGAVDVKLVLNPRAFSAEIREGWEIYRDEFWAREGARRRKQAHELRPKSE
+  best_structure_probability: 1.0
+  transmembrane_segments: 
+  - aaseq: WQFTLFLASMAGVGAFTFYEL
+    stop: 93
+    start: 73
+    probability: 1.0
+  - aaseq: VILQFTLSFISITVVLFHISG
+    stop: 126
+    start: 106
+    probability: 1.0
+  num_certain_transmembrane_segments: 2
+  num_found: 2
+YAL008W: 
+  num_putative_transmembrane_segments: 0
+  aaseq: MTLAFNMQRLVFRNLNVGKRMFKNVPLWRFNVANKLGKPLTRSVGLGGAGIVAGGFYLMNRQPSKLIFNDSLGAAVKQQGPLEPTVGNSTAITEERRNKISSHKQMFLGSLFGVVLGVTVAKISILFMYVGITSMLLCEWLRYKGWIRINLKNIKSVIVLKDVDLKKLLIDGLLGTEYMGFKVFFTLSFVLASLNANK
+  best_structure_probability: 1.0
+  transmembrane_segments: 
+  - aaseq: LTRSVGLGGAGIVAGGFYLMN
+    stop: 60
+    start: 40
+    probability: 1.0
+  - aaseq: AKISILFMYVGITSMLLCEWL
+    stop: 141
+    start: 121
+    probability: 1.0
+  - aaseq: TEYMGFKVFFTLSFVLASLNA
+    stop: 196
+    start: 176
+    probability: 1.0
+  num_certain_transmembrane_segments: 3
+  num_found: 3
+YAL007C: 
+  num_putative_transmembrane_segments: 0
+  aaseq: MIKSTIALPSFFIVLILALVNSVAASSSYAPVAISLPAFSKECLYYDMVTEDDSLAVGYQVLTGGNFEIDFDITAPDGSVITSEKQKKYSDFLLKSFGVGKYTFCFSNNYGTALKKVEITLEKEKTLTDEHEADVNNDDIIANNAVEEIDRNLNKITKTLNYLRAREWRNMSTVNSTESRLTWLSILIIIIIAVISIAQVLLIQFLFTGRQKNYV
+  best_structure_probability: 1.0
+  transmembrane_segments: 
+  - aaseq: STIALPSFFIVLILALVNSVA
+    stop: 24
+    start: 4
+    probability: 1.0
+  - aaseq: LTWLSILIIIIIAVISIAQVL
+    stop: 201
+    start: 181
+    probability: 1.0
+  num_certain_transmembrane_segments: 2
+  num_found: 2
+YAL005C: 
+  num_putative_transmembrane_segments: 1
+  aaseq: MSKAVGIDLGTTYSCVAHFANDRVDIIANDQGNRTTPSFVAFTDTERLIGDAAKNQAAMNPSNTVFDAKRLIGRNFNDPEVQADMKHFPFKLIDVDGKPQIQVEFKGETKNFTPEQISSMVLGKMKETAESYLGAKVNDAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKGKEEHVLIFDLGGGTFDVSLLFIEDGIFEVKATAGDTHLGGEDFDNRLVNHFIQEFKRKNKKDLSTNQRALRRLRTACERAKRTLSSSAQTSVEIDSLFEGIDFYTSITRARFEELCADLFRSTLDPVEKVLRDAKLDKSQVDEIVLVGGSTRIPKVQKLVTDYFNGKEPNRSINPDEAVAYGAAVQAAILTGDESSKTQDLLLLDVAPLSLGIETAGGVMTKLIPRNSTISTKKFEIFSTYADNQPGVLIQVFEGERAKTKDNNLLGKFELSGIPPAPRGVPQIEVTFDVDSNGILNVSAVEKGTGKSNKITITNDKGRLSKEDIEKMVAEAEKFKEEDEKESQRIASKNQLESIAYSLKNTISEAGDKLEQADKDTVTKKAEETISWLDSNTTASKEEFDDKLKELQDIANPIMSKLYQAGGAPGGAAGGAPGGFPGGAPPAPEAEGPTVEEVD
+  best_structure_probability: 1.0
+  transmembrane_segments: 
+  - aaseq: AGGAPGGAAGGAPGGFPGGAP
+    stop: 628
+    start: 608
+    probability: 1.0
+  num_certain_transmembrane_segments: 1
+  num_found: 2
+YAL004W: 
+  num_putative_transmembrane_segments: 1
+  aaseq: MGVTSGGLNFKDTVFNEQQRDIESTTTQVENQDVFFLTLLVQTVSNGSGGRFVNNTQDIQTSNGTSILGSLSLRIVEVSWDSDDSVIDLGSQVRFGSFLHLTQDHGGDLFWGKVLGFTLKFNLNLRLTVNIDQLEWEVLHVSLHFWVVEVSTDQTLSVENGIRRIHSSLILSSITNQSFSVSESDKRWSGSVTLIVGNNVHTIISKVSNTRVCCT
+  best_structure_probability: 0.06
+  transmembrane_segments: 
+  - aaseq: QDVFFLTLLVQTVSNGSGGRF
+    stop: 52
+    start: 32
+    probability: 0.06
+  num_certain_transmembrane_segments: 0
+  num_found: 1
+YAL003W: 
+  aaseq: MASTDFSKIETLKQLNASLADKSYIEGTAVSQADVTVFKAFQSAYPEFSRWFNHIASKADEFDSFPAASAAAAEEEEDDDVDLFGSDDEEADAEAEKLKAERIAAYNAKKAAKPAKPAAKSIVTLDVKPWDDETNLEEMVANVKAIEMEGLTWGAHQFIPIGFGIKKLQINCVVEDDKVSLDDLQQSIEEDEDHVQSTDIAAMQKL
+  num_found: 0
+YAL014C: 
+  num_putative_transmembrane_segments: 0
+  aaseq: MDVLKLGYELDQLSDLVEERTRLVSVLKLAPTSNDNVTLKRQLGSILELLQKCAPNDELISRYNTILDKIPDTAVDKELYRFQQQVARNTDEVSKESLKKVRFKNDDELTVMYKDDDEQDEESPLPSTHTPYKDEPLQSQLQSQSQPQPPQPMVSNQELFINQQQQLLEQDSHLGALSQSIGRTHDISLDLNNEIVSQNDSLLVDLENLIDNNGRNLNRASRSMHGFNNSRFKDNGNCVIILVLIVVLLLLLLVL
+  best_structure_probability: 1.0
+  transmembrane_segments: 
+  - aaseq: NGNCVIILVLIVVLLLLLLVL
+    stop: 255
+    start: 235
+    probability: 1.0
+  num_certain_transmembrane_segments: 1
+  num_found: 1
+YAL013W: 
+  num_putative_transmembrane_segments: 1
+  aaseq: MSQQTPQESEQTTAKEQDLDQESVLSNIDFNTDLNHNLNLSEYCISSDAGTEKMDSDEEKSLANLPELKYAPKLSSLVKQETLTESLKRPHEDEKEAIDEAKKMKVPGENEDESKEEEKSQELEEAIDSKEKSTDARDEQGDEGDNEEENNEEDNENENEHTAPPALVMPSPIEMEEQRMTALKEITDIEYKFAQLRQKLYDNQLVRLQTELQMCLEGSHPELQVYYSKIAAIRDYKLHRAYQRQKYELSCINTETIATRTFIHQDFHKKVTDLRARLLNRTTQTWYDINKERRDMDIVIPDVNYHVPIKLDNKTLSCITGYASAAQLCYPGEPVAEDLACESIEYRYRANPVDKLEVIVDRMRLNNEISDLEGLRKYFHSFPGAPELNPLRDSEINDDFHQWAQCDRHTGPHTTSFCYS
+  best_structure_probability: 0.08
+  transmembrane_segments: 
+  - aaseq: KTLSCITGYASAAQLCYPGEP
+    stop: 334
+    start: 314
+    probability: 0.08
+  num_certain_transmembrane_segments: 0
+  num_found: 1
+YAL002W: 
+  num_putative_transmembrane_segments: 2
+  aaseq: MEQNGLDHDSRSSIDTTINDTQKTFLEFRSYTQLSEKLASSSSYTAPPLNEDGPKGVASAVSQGSESVVSWTTLTHVYSILGAYGGPTCLYPTATYFLMGTSKGCVLIFNYNEHLQTILVPTLSEDPSIHSIRSPVKSIVICSDGTHVAASYETGNICIWNLNVGYRVKPTSEPTNGMTPTPALPAVLHIDDHVNKEITGLDFFGARHTALIVSDRTGKVSLYNGYRRGFWQLVYNSKKILDVNSSKEKLIRSKLSPLISREKISTNLLSVLTTTHFALILLSPHVSLMFQETVEPSVQNSLVVNSSISWTQNCSRVAYSVNNKISVISISSSDFNVQSASHSPEFAESILSIQWIDQLLLGVLTISHQFLVLHPQHDFKILLRLDFLIHDLMIPPNKYFVISRRSFYLLTNYSFKIGKFVSWSDITLRHILKGDYLGALEFIESLLQPYCPLANLLKLDNNTEERTKQLMEPFYNLSLAALRFLIKKDNADYNRVYQLLMVVVRVLQQSSKKLDSIPSLDVFLEQGLEFFELKDNAVYFEVVANIVAQGSVTSISPVLFRSIIDYYAKEENLKVIEDLIIMLNPTTLDVDLAVKLCQKYNLFDLLIYIWNKIFDDYQTPVVDLIYRISNQSEKCVIFNGPQVPPETTIFDYVTYILTGRQYPQNLSISPSDKCSKIQRELSAFIFSGFSIKWPSNSNHKLYICENPEEEPAFPYFHLLLKSNPSRFLAMLNEVFEASLFNDDNDMVASVGEAELVSRQYVIDLLLDAMKDTGNSDNIRVLVAIFIATSISKYPQFIKVSNQALDCVVNTICSSRVQGIYEISQIALESLLPYYHSRTTENFILELKEKNFNKVLFHIYKSENKYASALSLILETKDIEKEYNTDIVSITDYILKKCPPGSLECGKVTEVIETNFDLLLSRIGIEKCVTIFSDFDYNLHQEILEVKNEETQQKYLDKLFSTPNINNKVDKRLRNLHIELNCKYKSKREMILWLNGTVLSNAESLQILDLLNQDSNFEAAAIIHERLESFNLAVRDLLSFIEQCLNEGKTNISTLLESLRRAFDDCNSAGTEKKSCWILLITFLITLYGKYPSHDERKDLCNKLLQEAFLGLVRSKSSSQKDSGGEFWEIMSSVLEHQDVILMKVQDLKQLLLNVFNTYKLERSLSELIQKIIEDSSQDLVQQYRKFLSEGWSIHTDDCEICGKKIWGAGLDPLLFLAWENVQRHQDMISVDLKTPLVIFKCHHGFHQTCLENLAQKPDEYSCLICQTESNPKIV
+  best_structure_probability: 1.0
+  transmembrane_segments: 
+  - aaseq: GAYGGPTCLYPTATYFLMGTS
+    stop: 102
+    start: 82
+    probability: 1.0
+  - aaseq: TNLLSVLTTTHFALILLSPHV
+    stop: 286
+    start: 266
+    probability: 1.0
+  - aaseq: KKSCWILLITFLITLYGKYPS
+    stop: 1092
+    start: 1072
+    probability: 1.0
+  num_certain_transmembrane_segments: 3
+  num_found: 5
+YAL012W: 
+  num_putative_transmembrane_segments: 0
+  aaseq: MTLQESDKFATKAIHAGEHVDVHGSVIEPISLSTTFKQSSPANPIGTYEYSRSQNPNRENLERAVAALENAQYGLAFSSGSATTATILQSLPQGSHAVSIGDVYGGTHRYFTKVANAHGVETSFTNDLLNDLPQLIKENTKLVWIETPTNPTLKVTDIQKVADLIKKHAAGQDVILVVDNTFLSPYISNPLNFGADIVVHSATKYINGHSDVVLGVLATNNKPLYERLQFLQNAIGAIPSPFDAWLTHRGLKTLHLRVRQAALSANKIAEFLAADKENVVAVNYPGLKTHPNYDVVLKQHRDALGGGMISFRIKGGAEAASKFASSTRLFTLAESLGGIESLLEVPAVMTHGGIPKEAREASGVFDDLVRISVGIEDTDDLLEDIKQALKQATN
+  best_structure_probability: 1.0
+  transmembrane_segments: 
+  - aaseq: QYGLAFSSGSATTATILQSLP
+    stop: 92
+    start: 72
+    probability: 1.0
+  num_certain_transmembrane_segments: 1
+  num_found: 1
+END
+
+MY_YAML2 = <<END_YAML2
+--- 
+SWN_SM33_HUMAN: 
+  aaseq: MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGGHSTV
+  num_found: 0
+SWN_UBP3_HUMAN: 
+  num_putative_transmembrane_segments: 1
+  transmembrane_segments: 
+  - aaseq: TMPGYGGAASAGASVFGASGL
+    stop: 724
+    start: 704
+    probability: 21.0
+  - aaseq: YELFAFISHMGTSTMSGHYIC
+    stop: 826
+    start: 806
+    probability: 21.0
+  aaseq: MQRRGALFGMPGGSGGRKMAAGDIGELLVPHMPTIRVPRSGDRVYKNECAFSYDSPNSEGGLYVCMNTFLAFGREHVERHFRKTGQSVYMHLKRHAREKVRGASGGALPKRRNSKIFLDLDTDDDLNSDDYEYEDEAKLVIFPDHYEIALPNIEELPALVTIACDAVLSSKSPYRKQDPDTWENELPVSKYANNLTQLDNGVRIPPSGWKCARCDLRENLWLNLTDGSVLCGKWFFDSSGGNGHALEHYRDMGYPLAVKLGTITPDGADVYSFQEEEPVLDPHLAKHLAHFGIDMLHMHGTENGLQDNDIKLRVSEWEVIQESGTKLKPMYGPGYTGLKNLGNSCYLSSVMQAIFSIPEFQRAYVGNLPRIFDYSPLDPTQDFNTQMTKLGHGLLSGQYSKPPVKSELIEQVMKEEHKPQQNGISPRMFKAFVSKSHPEFSSNRQQDAQEFFLHLVNLVERNRIGSENPSDVFRFLVEERIQCCQTRKVRYTERVDYLMQLPVAMEAATNKDELIAYELTRREAEANRRPLPELVRAKIPFSACLQAFSEPENVDDFWSSALQAKSAGVKTSRFASFPEYLVVQIKKFTFGLDWVPKKFDVSIDMPDLLDINHLRARGLQPGEEELPDISPPIVIPDDSKDRLMNQLIDPSDIDESSVMQLAEMGFPLEACRKAVYFTGNMGAEVAFNWIIVHMEEPDFAEPLTMPGYGGAASAGASVFGASGLDNQPPEEIVAIITSMGFQRNQAIQALRATNNNLERALDWIFSHPEFEEDSDFVIEMENNANANIISEAKPEGPRVKDGSGTYELFAFISHMGTSTMSGHYICHIKKEGRWVIYNDHKVCASERPPKDLGYMYFYRRIPS
+  num_certain_transmembrane_segments: 2
+  num_found: 3
+SWN_UBPN_HUMAN: 
+  num_putative_transmembrane_segments: 3
+  transmembrane_segments: 
+  - aaseq: PSSTSSASALYGQPLLLSVPK
+    stop: 556
+    start: 536
+    probability: 21.0
+  aaseq: MYNVGEHNLFPGPIDNSGLFSDPESQTLKEHLIDELDYVLVPTEAWNKLLNWYGCVEGQQPIVRKVVEHGLFVKHCKVEVYLLELKLCENSDPTNVLSCHFSKADTIATIEKEMRKLFNIPAERETRLWNKYMSNTYEQLSKLDNTVQDAGLYQGQVLVIEPQNEDGTWPRQTLQSKSSTAPSRNFTTSPKSSASPYSSVSASLIANGDSTSTCGMHSSGVSRGGSGFSASYNCQEPPSSHIQPGLCGLGNLGNTCFMNSALQCLSNTHPLTDYFLKDEYEAEINRDNPLGMKGEIAEAYAELIKQMWSGRDAHVAPWMFKTQVGRFAPQFSGYQQQDSQELLAFPSRWIHEDLNRVKKKPYLELKDANGRPDAVVAKEAWENHRLRNDSVIVDTFHGLFKSTLVCPECAKVSVTFDPFCYLTLPLPLKKDRVMEVFLVPADPHCRPTQYRVTVPLMGAVSDLCEALSRLSGIAAENMVVADVYNHRFHKIFQMDEGLNHIMPRDDIFVYEVCSTSVDGSECVTLPVYFRERKSRPSSTSSASALYGQPLLLSVPKHKLTLESLYQAVCDRISRYVKQPLPDEFGSSPLEPGACNGSRNSCEGEDEEEMEHQEEGKEQLSETEGSGEDEPGNDPSETTQKKIKGQPCPKRLFTFSLVNSYGTADINSLAADGKLLKLNSRSTLAMDWDRETRRLYYDEQESEAYEKHVSMLQPQKKKKTTVALRDCIELFTTMETLGEHDPWYCPNCKKHQQATKKFDLWSLPKILVVHLKRFSYNRYWRDKLDTVVEFPIRGLNMSEFVCNLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSWPLRIR
+  num_certain_transmembrane_segments: 0
+  num_found: 3
+SWN_PWP1_HUMAN: 
+  num_putative_transmembrane_segments: 0
+  transmembrane_segments: 
+  - aaseq: MGVLFCSSCCPDLPFIYAFGG
+    stop: 450
+    start: 430
+    probability: 21.0
+  aaseq: MNRSRQVTCVAWVRCGVAKETPDKVELSKEEVKRLIAEAKEKLQEEGGGSDEEETGSPSEDGMQSARTQARPREPLEDGDPEDDRTLDDDELAEYDLDKYDEEGDPDAETLGESLLGLTVYGSNDQDPYVTLKDTEQYEREDFLIKPSDNLIVCGRAEQDQCNLEVHVYNQEEDSFYVHHDILLSAYPLSVEWLNFDPSPDDSTGNYIAVGNMTPVIEVWDLDIVDSLEPVFTLGSKLSKKKKKKGKKSSSAEGHTDAVLDLSWNKLIRNVLASASADNTVILWDMSLGKPAASLAVHTDKVQTLQFHPFEAQTLISGSYDKSVALYDCRSPDESHRMWRFSGQIERVTWNHFSPCHFLASTDDGFVYNLDARSDKPIFTLNAHNDEISGLDLSSQIKGCLVTASADKYVKIWDILGDRPSLVHSRDMKMGVLFCSSCCPDLPFIYAFGGQKEGLRVWDISTVSSVNEAFGRRERLVLGSARNSSISGPFGSRSSDTPMES
+  num_certain_transmembrane_segments: 1
+  num_found: 1
+SW_FGF7_HUMAN: 
+  num_putative_transmembrane_segments: 0
+  transmembrane_segments: 
+  - aaseq: RSCFHIICLVGTISLACNDMT
+    stop: 36
+    start: 16
+    probability: 21.0
+  aaseq: MHKWILTWILPTLLYRSCFHIICLVGTISLACNDMTPEQMATNVNCSSPERHTRSYDYMEGGDIRVRRLFCRTQWYLRIDKRGKVKGTQEMKNNYNIMEIRTVAVGIVAIKGVESEFYLAMNKEGKLYAKKECNEDCNFKELILENHYNTYASAKWTHNGGEMFVALNQKGIPVRGKKTKKEQKTAHFLPMAIT
+  num_certain_transmembrane_segments: 1
+  num_found: 1
+SWN_SM31_HUMAN: 
+  aaseq: MSEEKPKEGVKTENDHINLKVAGQDGSVVQFKIKRHTSLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLRMEDEDTIDVFQQQTGGVPESSLAGHSF
+  num_found: 0
+SWN_UFD1_HUMAN: 
+  aaseq: MFSFNMFDHPIPRVFQNRFSTQYRCFSVSMLAWPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEDGLVQLETVNLQVATYSKSKFCYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSADFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIHECDMNVDFDAPLGYKEPERQVQHEESTEGEADHSGYAGELGFRAFSGSGNRLDGKKKGVEPSPSPIKPGDIKRGIPNYEFKLGKITFIRNSRPLVKKVEEDEAGGRFVAFSGEGQSLRKKGRKP
+  num_found: 0
+SWN_UBCE_HUMAN: 
+  aaseq: MNSNVENLPPHIIRLVYKEVTTLTADPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGLFRMKLLLGKDFPASPPKGYFLTKIFHPNVGANGEICVNVLKRDWTAELGIRHVLLTIKCLLIHPNPESALNEEAGRLLLENYEEYAARARLLTEIHGGAGGPSGRAEAGRALASGTEASSTDPGAPGGPGGAEGPMAKKHAGERDKKLAAKKKTDKKRALRALRRL
+  num_found: 0
+SWN_K1CL_HUMAN: 
+  num_putative_transmembrane_segments: 0
+  transmembrane_segments: 
+  - aaseq: GSAFGFGASCGGGFSAASMFG
+    stop: 64
+    start: 44
+    probability: 21.0
+  - aaseq: ALGGGSFGGLGMGFGGSPGGG
+    stop: 108
+    start: 88
+    probability: 21.0
+  aaseq: MDLSNNTMSLSVRTPGLSRRLSSQSVIGRPRGMSASSVGSGYGGSAFGFGASCGGGFSAASMFGSSSGFGGGSGSSMAGGLGAGYGRALGGGSFGGLGMGFGGSPGGGSLGILSGNDGGLLSGSEKETMQNLNDRLASYLDKVRALEEANTELENKIREWYETRGTGTADASQSDYSKYYPLIEDLRNKIISASIGNAQLLLQIDNARLAAEDFRMKYENELALRQGVEADINGLRRVLDELTLTRTDLEMQIESLNEELAYMKKNHEDELQSFRVGGPGEVSVEMDAAPGVDLTRLLNDMRAQYETIAEQNRKDAEAWFIEKSGELRKEISTNTEQLQSSKSEVTDLRRAFQNLEIELQSQLAMKKSLEDSLAEAEGDYCAQLSQVQQLISNLEAQLLQVRADAERQNVDHQRLLNVKARLELEIETYRRLLDGEAQGDGLEESLFVTDSKSQAQSTDSSKDPTKTRKIKTVVQEMVNGEVVSSQVQEIEELM
+  num_certain_transmembrane_segments: 2
+  num_found: 2
+SWN_UBCC_HUMAN: 
+  aaseq: MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI
+  num_found: 0
+SWN_SM32_HUMAN: 
+  aaseq: MADEKPKEGVKTENNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGVY
+  num_found: 0
+END_YAML2
+
+end
+
+
+

data/specs/transmem_spec.rb

@@ -0,0 +1,60 @@
+require File.expand_path( File.dirname(__FILE__) + '/spec_helper' )
+require File.expand_path( File.dirname(__FILE__) + '/transmem_spec_shared' )
+require 'transmem'
+
+# turns all string keys into symbol keys
+def string_to_symbol(hash)
+  if hash.is_a? Hash
+    hash.each do |k,v|
+      hash[k.to_sym] = hash.delete(k)
+      if v.is_a? Hash
+        string_to_symbol(v)
+      elsif v.is_a? Array
+        v.each do |armemb|
+          string_to_symbol(armemb)
+        end
+      end
+    end
+  end
+end
+
+describe TransmemIndex, "determining filetypes" do
+  before(:each) do
+    @files = %w(toppred.small.out toppred.xml.out phobius.small.small.txt phobius.small.noheader.txt).map {|f| Tfiles + '/' + f }
+    @types = %w(toppred toppred phobius phobius).map {|v| v.to_sym }
+    @classes = %w(TopPred TopPred Phobius Phobius).map {|v| v.to_sym }
+  end
+  it 'figures out the filetype' do
+    @files.zip(@types) do |file,tp|
+      TransmemIndex.filetype(file).should == tp
+    end
+  end
+  it 'given a file to initalize, returns the right object' do
+    objects = @files.zip(@classes) do |file,base_klass|
+      obj = TransmemIndex.new(file)
+      base = Kernel.const_get(base_klass)
+      klass = base.const_get(:Index)
+      obj.class.should == klass
+    end
+  end
+end
+
+
+
+describe TransmemIndex, "methods" do
+  it 'calculates the num of overlapping chars in start/stop seqs' do
+    ##########0         1         2         3         4         5         6
+    ##########01234567890123456789012345678901234567890123456789012345678901
+    ##########   ****         ****                       **   ***
+    string = 'ABCDEFG ABCDEFG ABCDEFG CATTITY ABCD EFG CD BCDEFGTTITY BCDEFG'
+    ########## ^^^^^^  ^^^^^^  ^^^^^^                     ^^^^^^      ^^^^^^
+    #         
+    substring = 'BCDEFG'
+    ranges = [(3..6), (16..19), (43..44), (48..50)]
+    expected = [4, 0, 3, 3, 0]
+    class TMshell ; include TransmemIndex ; end
+    TMshell.new.num_overlapping_chars(string, ranges, substring).should == expected
+  end
+end
+
+

data/specs/transmem_spec_shared.rb

@@ -0,0 +1,64 @@
+
+# turns all string keys into symbol keys
+def string_to_symbol(hash)
+  if hash.is_a? Hash
+    hash.each do |k,v|
+      hash[k.to_sym] = hash.delete(k)
+      if v.is_a? Hash
+        string_to_symbol(v)
+      elsif v.is_a? Array
+        v.each do |armemb|
+          string_to_symbol(armemb)
+        end
+      end
+    end
+  end
+end
+
+
+
+describe "a transmem index", :shared => true do
+  before(:all) do
+    # expects an transmem object, @obj
+  end
+
+  it 'is a hash' do
+    @obj.is_a?(Hash).should be_true
+  end
+
+  it 'responds to reference_to_key' do
+    @obj.respond_to?(:reference_to_key).should be_true
+  end
+
+  it "correctly transforms headers or refs into id's" do
+    @ref_to_key.each do |k,v|
+      @obj.reference_to_key(k).should == v
+    end
+  end
+
+  it "creates a num_certain_index that gives correct values given keys" do
+    ind = @obj.num_certain_index
+    @test_hash.each do |k,v|
+      ind[@obj.reference_to_key(k)].should == v
+    end
+  end
+end
+
+
+describe "a calculator of transmembrane overlap", :shared => true do
+  # require definition of @tm_test and @obj
+  
+  it "can give average overlap given a sequence (fraction)" do
+    [:number, :fraction].each do |tp|
+    #[:fraction, :number].each do |tp|
+      hash = @tm_test
+      key = hash[:mykey]
+      hash[:seqs].zip(hash[:exps][tp]) do |seq,exp|
+        @obj.avg_overlap(key, seq, tp).should == exp
+      end
+    end
+  end
+
+end
+
+

data/specs/validator/aa_spec.rb

@@ -0,0 +1,107 @@
+require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
+require File.expand_path( File.dirname(__FILE__) + '/../validator_helper' )
+
+
+require 'validator/aa'
+require 'spec_id'
+require 'spec_id/digestor'
+
+klass = Validator::AA
+
+class MyAA < Validator::AA ; def initialize ; end ; end
+
+describe klass, "using frequency estimates" do
+  before(:each) do
+    @small_fasta = Tfiles + '/small.fasta'
+    @sequest_params = Tfiles + '/bioworks32.params'
+    #         C/D      C/D    J     (7)
+    @seqs = %w(ABCDEFGC CCDCCC JJJJJ XYZ WXXXYZ TXXXXXYZ ZZXIIPTYZ ZZXTYZZ ZZZZ YYYYYTL)
+    @peps =  @seqs.map {|n| v = SpecID::GenericPep.new; v.aaseq = n ; v }
+    val = klass.new('C')
+    val.frequency = 0.11
+    @validator = val
+  end
+  #C: 0.0157714433456144
+  #D: 0.0526145691939758
+
+  it_should_behave_like 'a validator'
+
+  it 'calculates precision from actual and expected correctly' do
+    MyAA.new.pephit_precision_from_actual_and_expected(5, 10, 100).should == 0.5
+    (0..10).each do |actual|
+      precision = MyAA.new.pephit_precision_from_actual_and_expected(actual, 10, 100)
+      answer = 1.0 - (actual.to_f/10.0)
+      precision.should be_close(answer, 0.00000001)
+      #0 -> 1
+      #1 -> 0.9
+      #2 -> 0.8
+    end
+  end
+
+  it 'calculates precision (with background) reasonably and consistently' do
+    (0..10).each do |bkg|
+      precision = MyAA.new.pephit_precision_from_actual_and_expected(5, 10, 100, bkg.to_f/100)
+      answer = 0.5 + bkg.to_f/10
+      answer = 1.0 if answer > 1.0 
+      precision.should == answer
+    end
+  end
+
+  it 'calculates at_least_one correctly' do
+    aa = 'C'
+    freq = 0.0157714433456144  ## from @small_fasta
+    (actual, expected) = MyAA.new.at_least_one(aa, freq, @seqs)
+    actual.should == 2
+    expected.should be_close(0.949318337979434, 0.0001)  # freeze for consistency
+  end
+
+  it 'gives consistent precision of peptides given fastafile and aa (even negative)' do
+    aa = 'C'
+    val = klass.new(aa).set_frequency(Fasta.new(@small_fasta))
+    # I checked this answer out by hand and it is correct
+    val.pephit_precision(@peps).should be_close(-1.10677, 0.001)
+  end
+end
+
+describe klass, "using empirical digestion data" do
+
+  before(:each) do
+    @small_fasta = Tfiles + '/small.fasta'
+    @sequest_params = Tfiles + '/bioworks32.params'
+    #         C/D      C/D    J     (7)
+    @seqs = %w(ABCDEFGC CCDCCC JJJJJ XYZ WXXXYZ TXXXXXYZ ZZXIIPTYZ ZZXTYZZ ZZZZ YYYYYTL)
+    @peps =  @seqs.map {|n| v = SpecID::GenericPep.new; v.aaseq = n ; v }
+
+    val = klass.new('C')
+    val.false_to_total_ratio = 0.22  # arbitrary
+    @validator = val
+  end
+
+  it_should_behave_like 'a validator'
+
+  it 'gives correct false to total ratio' do
+    aa = 'C'
+    val = klass.new(aa)
+    peptides = Digestor.digest( Fasta.new(@small_fasta), Sequest::Params.new(@sequest_params))
+    val.set_false_to_total_ratio( peptides )
+    # frozen (but I checked the peptides by hand to make sure they were
+    # correct)
+    val.false_to_total_ratio.should be_close(0.177629264861062, 0.0000000000001)
+  end
+
+  it 'can validate with theoretical digestion or frequency estimate' do
+    aa = 'C'
+    val = klass.new(aa)
+    val.false_to_total_ratio = 0.177629264861062
+    answ = val.pephit_precision(@peps)
+    # frozen
+    answ.should be_close(-0.125940594059407, 0.0000000001)
+
+    val.frequency = 0.0157714433456144  ## from @small_fasta
+    val.false_to_total_ratio = nil
+    answ = val.pephit_precision(@peps)
+    answ.should be_close(-1.10677485094924, 0.0000000001)
+  end
+end
+
+

data/specs/validator/background_spec.rb

@@ -0,0 +1,51 @@
+require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
+
+require 'validator/background'
+
+describe Validator::Background do
+
+  before(:all) do
+    @expected = YAML.load("badAA: 45
+tpred-1: 36
+tpred-1-0.8: 36
+tpred-2: 36
+tpred-2-0.8: 36
+phob-1: 38
+phob-2: 37
+phob-1-0.8: 38
+phob-2-0.8: 37
+bias-mrna: 29
+bias-prot: 37
+")
+@data = 
+  { 
+    'badAA' => [0.158873276514528, 0.15968405463222, 0.159870678279229, 0.159635650410558, 0.156543159883917, 0.152783096042051, 0.150294985250737, 0.145335608646189, 0.134808758575322, 0.125552050473186, 0.112790697674419, 0.0960860693748841, 0.076310861423221, 0.0560216123986919, 0.0388044914134742, 0.0250922509225092, 0.0187774670395525, 0.0111182381868719, 0.00934787447139996, 0.00583022388059702, 0.00460382844681367, 0.00348518795120737, 0.00284164298630845, 0.0021488047273704, 0.00167177486765116, 0.00175080245112343, 0.00182926829268293, 0.00191570881226054, 0.0016767270288397, 0.00177116542685087, 0.00186219739292365, 0.00198491464867011, 0.00211864406779661, 0.00136986301369863, 0.00146412884333821, 0.00107642626480086, 0.00120336943441637, 0.000672494956287828, 0.000764525993883792, 0.000887311446317658, 0.00103734439834025, 0.00123609394313968, 0.00151975683890578, 0.00179856115107914, 0.00215982721382289, 0.00266666666666667, 0.0, 0.0, 0.0, 0.0, 0.0/0.0],
+    'tpred-1-0.8' => [0.432087342709104, 0.430464886251236, 0.432952622673435, 0.430709911544568, 0.431700713758307, 0.426344086021505, 0.42326139088729, 0.412998624484182, 0.405773857257418, 0.395963479096588, 0.379389752446747, 0.375838926174497, 0.371165644171779, 0.366496598639456, 0.351903435468895, 0.337611056268509, 0.334031413612565, 0.332236842105263, 0.335585585585586, 0.334894613583138, 0.33133971291866, 0.334558823529412, 0.331658291457286, 0.328998699609883, 0.330175913396482, 0.334745762711864, 0.332844574780059, 0.327188940092166, 0.317152103559871, 0.320689655172414, 0.323583180987203, 0.324271844660194, 0.322245322245322, 0.317180616740088, 0.324644549763033, 0.323834196891192, 0.32183908045977, 0.327044025157233, 0.316363636363636, 0.311203319502075, 0.314553990610329, 0.318918918918919, 0.306122448979592, 0.307086614173228, 0.295238095238095, 0.255555555555556, 0.246753246753247, 0.254237288135593, 0.290322580645161, 0.3, 0.0/0.0],
+    'tpred-2-0.8' => [0.193930421909697, 0.194460929772502, 0.193104906937394, 0.188931730551145, 0.187792271720404, 0.181989247311828, 0.176558752997602, 0.172627235213205, 0.168003207698476, 0.157135992311389, 0.145653425446172, 0.136241610738255, 0.125766871165644, 0.122448979591837, 0.115134633240483, 0.107601184600197, 0.103664921465969, 0.103070175438596, 0.102477477477477, 0.101873536299766, 0.101674641148325, 0.10171568627451, 0.101758793969849, 0.0988296488946684, 0.0987821380243572, 0.100282485875706, 0.095307917888563, 0.0921658986175115, 0.0809061488673139, 0.0793103448275862, 0.0822669104204753, 0.0757281553398058, 0.079002079002079, 0.0814977973568282, 0.0853080568720379, 0.0803108808290155, 0.0718390804597701, 0.0786163522012579, 0.0836363636363636, 0.0746887966804979, 0.07981220657277, 0.0756756756756757, 0.0748299319727891, 0.062992125984252, 0.0666666666666667, 0.0555555555555556, 0.025974025974026, 0.0338983050847458, 0.032258064516129, 0.0, 0.0/0.0],
+    'tpred-1' => [0.43492586490939, 0.434656516222585, 0.437751004016064, 0.439366015481017, 0.435423665546846, 0.432272813869308, 0.432531593966572, 0.422057502246181, 0.419948186528497, 0.413091136861885, 0.395751376868607, 0.39067055393586, 0.379793061472915, 0.378066378066378, 0.366721854304636, 0.348222424794895, 0.34251968503937, 0.339958158995816, 0.343073593073593, 0.343502824858757, 0.337587006960557, 0.33969010727056, 0.336196319018405, 0.332909783989835, 0.334656084656085, 0.339779005524862, 0.339055793991416, 0.331831831831832, 0.323343848580442, 0.326050420168067, 0.329181494661922, 0.330170777988615, 0.325865580448065, 0.321814254859611, 0.326340326340326, 0.322250639386189, 0.320113314447592, 0.325077399380805, 0.314285714285714, 0.308943089430894, 0.311926605504587, 0.317460317460317, 0.304635761589404, 0.305343511450382, 0.293577981651376, 0.258064516129032, 0.253164556962025, 0.262295081967213, 0.303030303030303, 0.333333333333333, 0.0/0.0],
+    'tpred-2' => [0.197144426139484, 0.197571143737539, 0.197699890470975, 0.195355694802801, 0.192422545726017, 0.191465040960183, 0.188544639217285, 0.185085354896676, 0.184974093264249, 0.176636392107736, 0.164044059795437, 0.154518950437318, 0.143639683505782, 0.137085137085137, 0.129966887417219, 0.113035551504102, 0.108267716535433, 0.105648535564854, 0.103896103896104, 0.105084745762712, 0.103248259860789, 0.103694874851013, 0.101840490797546, 0.0991105463786531, 0.0992063492063492, 0.100828729281768, 0.0958512160228898, 0.0930930930930931, 0.082018927444795, 0.0789915966386555, 0.0818505338078292, 0.0759013282732448, 0.0794297352342159, 0.08207343412527, 0.0839160839160839, 0.0792838874680307, 0.0708215297450425, 0.0773993808049536, 0.0821428571428571, 0.0731707317073171, 0.0779816513761468, 0.0740740740740741, 0.0728476821192053, 0.0610687022900763, 0.0642201834862385, 0.0537634408602151, 0.0253164556962025, 0.0327868852459016, 0.0303030303030303, 0.0, 0.0/0.0],
+    'phob-1-0.8' => [0.185672175669857, 0.18433572392246, 0.181897765767137, 0.178760843645932, 0.176211849192101, 0.17261698440208, 0.168649249583102, 0.164665082525207, 0.158626390141268, 0.149688712442479, 0.140255798829395, 0.127386902473408, 0.116115516983391, 0.106017191977077, 0.0974025974025974, 0.0923076923076923, 0.0875342754693103, 0.0849369608493696, 0.0839240795792362, 0.0830359267190102, 0.0802955665024631, 0.0777188998233661, 0.0760188087774295, 0.0748373101952278, 0.0739595050618673, 0.0732568402471315, 0.0716041794714198, 0.070096463022508, 0.0682432432432432, 0.0678329168154231, 0.0672174239579422, 0.0656262505002001, 0.0652173913043478, 0.0629306384933395, 0.0637567435017165, 0.0637837837837838, 0.0609903381642512, 0.0594193112761648, 0.0598618572524942, 0.0587711487088157, 0.059375, 0.0619578686493185, 0.0609756097560976, 0.0576576576576577, 0.0497835497835498, 0.0427807486631016, 0.043010752688172, 0.0396039603960396, 0.0504201680672269, 0.075, 0.0/0.0],
+    'phob-2-0.8' => [0.10336833040771, 0.10306752822552, 0.102234232862635, 0.099946552645644, 0.0978007181328546, 0.0957662787818767, 0.0927181767648694, 0.0913878363624687, 0.0879921851517884, 0.0834611567265181, 0.0773899848254932, 0.0688196847366398, 0.0604518928624869, 0.0551154559244901, 0.050834879406308, 0.0477522477522478, 0.0438726007171483, 0.0433532404335324, 0.042305053738852, 0.0418748512966928, 0.0399014778325123, 0.0386071158213475, 0.0378787878787879, 0.0366052060737527, 0.0357142857142857, 0.0344218887908208, 0.0331899200983405, 0.0327974276527331, 0.0307432432432432, 0.0307033202427704, 0.0311678558017274, 0.0300120048019208, 0.0294117647058824, 0.0257234726688103, 0.0264835703776361, 0.0264864864864865, 0.0241545893719807, 0.0229574611748818, 0.0230237912509593, 0.0231522707034728, 0.025, 0.0285006195786865, 0.0274390243902439, 0.0234234234234234, 0.0238095238095238, 0.018716577540107, 0.021505376344086, 0.0247524752475248, 0.0336134453781513, 0.05, 0.0/0.0],
+    'phob-1' => [0.189416875082269, 0.188798733425688, 0.187119003445534, 0.186618069952518, 0.184998809969059, 0.183175272216368, 0.18173689504862, 0.178471651602301, 0.173068705189687, 0.166212849776954, 0.156364435330306, 0.146373298526944, 0.134995296331138, 0.119743406985032, 0.107213765718068, 0.0987060998151571, 0.0901459124525285, 0.0851336898395722, 0.0844097995545657, 0.083527764815679, 0.0809500727096461, 0.077191235059761, 0.0762076982691811, 0.075208165457964, 0.0743939816104765, 0.0735337029471841, 0.0719512195121951, 0.070242656449553, 0.06841046277666, 0.0680127523910733, 0.0674115456238361, 0.0658991663358476, 0.0656779661016949, 0.0634703196347032, 0.063933626159102, 0.0640473627556512, 0.0613718411552347, 0.0598520511096167, 0.0603975535168196, 0.059449866903283, 0.0601659751037344, 0.0618046971569839, 0.060790273556231, 0.0575539568345324, 0.0496760259179266, 0.0426666666666667, 0.0428571428571429, 0.0396039603960396, 0.0504201680672269, 0.075, 0.0/0.0],
+    'phob-2' => [0.106884296432802, 0.106174549772412, 0.105618870924993, 0.10492877683408, 0.103770698038149, 0.102774850720056, 0.101225736746023, 0.0991783073130649, 0.0961967617871896, 0.0911882277967673, 0.0851765050534642, 0.0778482192802536, 0.0702022577610536, 0.06143977191732, 0.0559232296492389, 0.0495378927911275, 0.0439736158305017, 0.0434224598930481, 0.0427616926503341, 0.042230517965469, 0.0399903053805138, 0.0383466135458167, 0.0379746835443038, 0.0367982809562181, 0.0359431596544999, 0.0347242486139481, 0.0335365853658537, 0.0328863346104725, 0.0308517773306506, 0.0308182784272051, 0.0312849162011173, 0.0301707026597856, 0.0296610169491525, 0.026027397260274, 0.0263543191800878, 0.0263724434876211, 0.0240673886883273, 0.0228648285137861, 0.0229357798165138, 0.0230700976042591, 0.024896265560166, 0.0284301606922126, 0.027355623100304, 0.0233812949640288, 0.0237580993520518, 0.0186666666666667, 0.0214285714285714, 0.0247524752475248, 0.0336134453781513, 0.05, 0.0/0.0],
+    'bias-mrna' => [0.433808285892922, 0.433569195326641, 0.433953549749274, 0.43349622685416, 0.433556050482554, 0.434016778640304, 0.42787610619469, 0.416422883146433, 0.400291326003195, 0.376082592486378, 0.340843023255814, 0.300129846039696, 0.250117041198502, 0.202474050902886, 0.159676354029062, 0.122878228782288, 0.0966839792249301, 0.077613855035279, 0.069441353216114, 0.0608675373134328, 0.0576690089653501, 0.0560119492158327, 0.0539912167398605, 0.0523771152296535, 0.0512677626079688, 0.0507732710825795, 0.0509146341463415, 0.0507662835249042, 0.0489604292421194, 0.0474672334396033, 0.0491620111731844, 0.0504168320762207, 0.0508474576271186, 0.0506849315068493, 0.0502684236212787, 0.0522066738428418, 0.0523465703971119, 0.0537995965030262, 0.0512232415902141, 0.0488021295474712, 0.0508298755186722, 0.0531520395550062, 0.0547112462006079, 0.0593525179856115, 0.060475161987041, 0.064, 0.0678571428571429, 0.0693069306930693, 0.0756302521008403, 0.05, 0.0/0.0],
+    'bias-prot' => [0.689591628549804, 0.689122922494652, 0.688836104513064, 0.68950500315814, 0.688229736113923, 0.685348278622898, 0.680862831858407, 0.669226393629124, 0.652805187482379, 0.628563234872383, 0.591351744186047, 0.547857540345019, 0.497542134831461, 0.441916678515569, 0.394319682959049, 0.359409594095941, 0.333799440671195, 0.316655976053025, 0.308479857556199, 0.297574626865672, 0.290041192149261, 0.284789644012945, 0.282097649186257, 0.279881815739995, 0.277514628030092, 0.278085789320105, 0.277743902439024, 0.278416347381865, 0.276659959758551, 0.275593340417995, 0.274115456238361, 0.268757443429933, 0.26864406779661, 0.265753424657534, 0.267935578330893, 0.263724434876211, 0.260529482551143, 0.255548083389375, 0.258409785932722, 0.266193433895297, 0.266597510373444, 0.279357231149567, 0.276595744680851, 0.26978417266187, 0.285097192224622, 0.272, 0.271428571428571, 0.262376237623762, 0.252100840336134, 0.3, 0.0/0.0],
+}
+  end
+
+
+
+  it 'finds the minimum of the plateu region of a stringency plot' do
+    #data = [10,11,12,10,9,8,7,6,5,4.5,4,3.4, 3.2, 3.3, 3.1, 3.0,2.9,2.8,2.8, 2.8, 2.9, 3.4, 2.2, 1.1,0.0,0.0/0.0]
+    #data = [10,11,12,10,9,8,7,6,5,4.5,4,3.4, 3.2, 3.3, 3.1, 3.0,2.9,2.8,2.8, 2.8, 2.9, 3.4, 2.2, 1.1,0.0]
+    @data.each do |k,v|
+      exp = @expected[k]
+      bkg = Validator::Background.new(v)
+      start_i = 25
+      stop_i = 38
+      ans =  bkg.min_mesa(start_i, stop_i)
+      ans.should be_close(v[exp], 0.01)
+      # expecting were my best judgement (erring on the min side)
+    end
+  end
+end