X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=slayer.cpp;h=9e5a61eaccfe04fdb079e105939bdb7d5be560a1;hb=8c1196586860f830fc9c813f2a79abab7434dc4b;hp=d838a2e86857bbce9a3375b795abe17964cbeaf0;hpb=05a0195e07c42c996592ee1c8abb63adedb7f493;p=mothur.git diff --git a/slayer.cpp b/slayer.cpp index d838a2e..9e5a61e 100644 --- a/slayer.cpp +++ b/slayer.cpp @@ -10,57 +10,456 @@ #include "slayer.h" /***********************************************************************/ -Slayer::Slayer(int win, int increment, int parentThreshold, float div) : - windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div) {} +Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i, int snp, int mi) : + minBS(mi), windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){ m = MothurOut::getInstance(); } /***********************************************************************/ -void Slayer::getResults(Sequence* query, vector refSeqs) { +string Slayer::getResults(Sequence* query, vector refSeqs) { try { + vector all; all.clear(); + myQuery = *query; + /*cout << "here" << endl; + query->setName("S000381746"); query->setAligned("...............................................................................................................................................A-C-GC--TGG-C--G-GC-A-GG--C----C-T--AACACA-T-GC-A-AGT-CGA-G-CG----------G-CAG-CG-G---------------------------GA-GG-A-AG----------------------------------------------------CTT-G----------------------------------------------------------------------------------CTT-CCTC----------------G-CC--G--GC--G--AG-C-GG-C-GG-A--C-------------GGG-TGAGT-A--AT-GT-C-T-G-GG---G-A--T-CT-G--C-C-CGA--TG-G------------------------------------------------------------------A-GG----GGG-AT-AA-CCA-------------------------C-T-G-----------------------GAA-A---CGG-TGG-CTAA-TA---CC-G--C-AT-A----------A--------------------C-------------------------------------GT-C-----------------------------------------------------------------------------------------------------------------------G-CA-A--------------------------------------------------------------------------------------------------------------------------------------G-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAA--G-T-G-GG-----G--GA-C--C--------------------------------------------------------------------------------------------------------------------TTC-G----------------------------------------------------------------------------------------------------------------------G-G--CC-TC--A---C-A--------------C----C-A---T-CG-G---AT---G-A-----A-CCC-AGA--T-GGG--A------TT--A--G-CT-A----G---TAGG-T-G-GG-G-T----AAT-GG-C-T-C-ACCT--A-GG-C-G--A-CG-A------------TCC-C-T------AG-CT-G-G-TCT-G-AG----A--GG-AT--G-AC-C-AG-CCAC-A-CTGGA--A-C-TG-A-GA-C-AC-G-G-TCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TTGCA-C-AA-T-GG--GC-GC-A----A-G-CC-T-GA-TG-CA-GCCA-TGCC-G-CG-T---G-T-G--T--GA-A-G--A--A-G-G-CC-----TT-CG---------G-G-T-T-G-T--A---AA-G-CAC--------TT-TC-A-G--C-GAG----GA-G--G---AA-GGTG---GTGA-GC----T--T--AA-T---A----------CG-CTCAT-CAA-TT-GA-CG-TT-A-C-TC-G-CA-G---------AA-----------GAAGC-ACC-GG-C-TAA---C--T-CCGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GG-AG-GGT-GCA-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GCGC-AC--G-CA-G-G-C-G------------G--T-TT-G-T-T-AA----G-T-C-A---G-ATG-TG-A-AA-TC--CC-CGA-G--------------------------------------------------------------------CT-T-AA-------------------------------------------------------------------------CT-T-G-GG-AA-C----T-G-C-A-T-T--------T--GA-A-A-C-T-G-GCA--A-G-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-A-G-A-G-T-C-----T-CG--TA-G-A------------G-GG-G-GG-T----AG--AATT-CCA-G-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAG-A-TC-T-GGA--GG-A-AT-A-CC-GG--T--G--GC-GAA-G--G-C---G----G--C-C-CCCTG------G-AC-GA--------------------------------------------------------------AG-A-C-T--GA--CG-----CT-CA-GG--T-G-CGA--AA-G-C--------------G-TGGG-GAG-C-A-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CA--C-G-CCG-T-AAA--C-GATG-TC--GA-TT---------T-GG--A--G-G-TT-G-TG-C--C--------------------------------------------------------------------------------------CTT-GA--------------------------------------------------------------------------------------------------------------------------------------------------G-G-C-GT--G-G-C-T-TC-C------GG--A----GC-TAA--CG-C-G-T--T--AA-AT--C----G-ACC-GCC-T-G-GG-GAG-TA---CGG-----C-C--G-C-A-A-GGT-T--AAA-ACTC-AAA---------TGAA-TTG-ACGGG-G-G-CCCG----C-A--C-A-A-GCG-GT-G--G--AG-CA-T--GT-GGT-TT-AATT-C-G-ATG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-TACTC-TT-G-AC-A-T-C--------------CAG-A-G-------------A-AC-T-T-T--CC--A-GA-G-A-T--G-G-A--T-T-G-G--T-G-----CC-------------------------------------T--TC-G------------------------------------------GG----A----A---CT-CTG---A--GA---------------------------------------------------C-A-G-G-T-GCTG-CA-TGG-CT--GTC-GTC-A-GC-TC---G-TG-TT-G--TGA-AA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-T-TA--TC--C-TTTG--T-T-G-C-C---AG-C-G--G--T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----C----C-G------------G----G---A-A--CT---------------C-A-A-A-G-GA-G--AC-T-G-CCA--G-T------------------------------------G-A---TAA----------------------------------A-C-T-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAGT-C---ATC-A-T-G-G-C-C-CTT----AC-G--AG-T-A-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-CGTA-T-A--C-AAA-GA-GA--------------------------------------------------------------------------------------------------A-G-C-G-A--ACCT-G-C--G---------------------------------------A-GG-G-C-----------A--A-G-CG---G----------A--CCT-C------A-T-AAAGT-AC-G-T-C-G-TAG-TCC--------GGA-T-TGGAG-TC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-ACTCC-A-T-G-AA-G-TC-GGAAT-CG-C-TA--G-TA-AT-C-G-T----AGA-TC-A-G--A------AT--GCT-AC-G-GT-G-AAT-ACGT-T-CCCGGGCCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-TG-GG-A--G---TGG-G-TT-GC-AAA--A-GAA------G--T-AGG-TA-G-C-T-T-AA-C-C-------------------------------------------------------------T-TC-G------------------------------------------------------------------------------------------------------GG-A--GG-G--C---GC-TTA--CC--ACT-T----T-GT.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................."); + refSeqs.resize(2); + refSeqs[1]->setName("S000381740"); refSeqs[1]->setAligned("...............................................................................................................................................a-c-gc--tgg-c--g-gc-a-gg--c----c-t--aacaca-t-gc-a-agt-cga-g-cg----------g-tag-ca-c----------------------------agga-g-ag----------------------------------------------------ctt-g----------------------------------------------------------------------------------ctc-tctg----------------g-gt--g--ac--g--ag-c-gg-c-gg-a--c-------------ggg-tgagt-a--at-gt-c-t-g-gg---a-a--a-ct-g--c-c-tga--tg-g------------------------------------------------------------------a-gg----ggg-at-aa-cta-------------------------c-t-g-----------------------gaa-a---cgg-tag-ctaa-ta---cc-g--c-at-a----------a--------------------c-------------------------------------gt-c-----------------------------------------------------------------------------------------------------------------------t-ac-g--------------------------------------------------------------------------------------------------------------------------------------g-a-c---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------caaa--g-t-g-gg-----g--ga-c--c--------------------------------------------------------------------------------------------------------------------ttc-g----------------------------------------------------------------------------------------------------------------------g-g--cc-tc--a---c-g--------------c----c-a---t-ca-g---at---g-t-----g-ccc-aga--t-ggg--a------tt--a--g-ct-a----g---tagg-t-g-gg-g-t----aat-gg-c-t-c-acct--a-gg-c-g--a-cg-a------------tcc-c-t------ag-ct-g-g-tct-g-ag----a--gg-at--g-ac-c-ag-ccac-a-ctgga--a-c-tg-a-ga-c-ac-g-g-tccaga-ctcc-tac-g--g-g-a-g-gc-a-gc-a-g-tg---gg-g-a-ata-ttgca-c-aa-t-gg--gc-gc-a----a-g-cc-t-ga-tg-ca-gcca-tgcc-g-cg-t---g-t-g--t--ga-a-g--a--a-g-g-cc-----tt-cg---------g-g-t-t-g-t--a---aa-g-cac--------tt-tc-a-g--c-gag----ga-g--g---aa-gggc---gatg-tc----t--t--aa-t---a----c-----gg-c-agc-gca-tt-ga-cg-tt-a-c-tc-g-ca-g---------aa-----------gaagc-acc-gg-c-taa---c--t-ccgt--gcca--g-c---a--gccg---c-gg--ta-at--ac---gg-ag-ggt-gca-a-g-cg-ttaa-t-cgg-aa-tt-a--c-t--gggc-gta----aa-gcgc-ac--g-ca-g-g-c-g------------g--t-tt-g-t-t-aa----g-t-c-a---g-atg-tg-a-aa-tc--cc-cgc-g--------------------------------------------------------------------ct-t-aa-------------------------------------------------------------------------cg-t-g-gg-aa-c----t-g-c-a-t-t--------t--ga-a-a-c-t-g-gca--a-g-c---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------t-a-g-a-g-t-c-----t-cg--ta-g-a------------g-gg-g-gg-t----ag--aatt-cca-g-gt--gt-a-gcg-gtgaaa-tg-cgt-agag-a-tc-t-gga--gg-a-at-a-cc-gg--t--g--gc-gaa-g--g-c---g----g--c-c-ccctg------g-ac-ga--------------------------------------------------------------ag-a-c-t--ga--cg-----ct-ca-gg--t-g-cga--aa-g-c--------------g-tggg-gag-c-a-aaca--gg-atta-g-ata-c-----cc-t-g-gta-g-t----c-ca--c-g-ctg-t-aaa--c-gatg-tc--ga-tt---------t-gg--a--g-g-tt-g-tg-c--c--------------------------------------------------------------------------------------ctt-ga--------------------------------------------------------------------------------------------------------------------------------------------------g-g-c-gt--g-g-c-t-tc-c------gg--a----gc-taa--cg-c-g-t--t--aa-at--c----g-acc-gcc-t-g-gg-gag-ta---cgg-----c-c--g-c-a-a-ggt-t--aaa-actc-aaa---------tgaa-ttg-acggg-g-g-cccg----c-a--c-a-a-gcg-gt-g--g--ag-ca-t--gt-ggt-tt-aatt-c-g-atg-caac-g-cg-a-ag-a-a-cc-tt-a-cc-tactc-tt-g-ac-a-t-c--------------cag-a-g-------------a-ac-t-t-t--cc--a-ga-g-a-t--g-g-a--t-t-g-g--t-g-----cc-------------------------------------t--tc-g------------------------------------------gg----a----a---ct-ctg---a--ga---------------------------------------------------c-a-g-g-t-gctg-ca-tgg-ct--gtc-gtc-a-gc-tc---g-tg-tt-g--tga-aa-tgt-t-gg-g-tt-aa-gt-cccgc-aa--------c-gag-cgc-a-acc-c-t-ta--tc--c-tttg--t-t-g-c-c---ag-c-g--a--t-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tcg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------g----t----c-g------------g----g---a-a--ct---------------c-a-a-a-g-ga-g--ac-t-g-ccg--g-t------------------------------------g-a---taa----------------------------------a-c-c-g--g-a-gg-a--agg-t--gggg-a-tgac-gtc--aagt-c---atc-a-t-g-g-c-c-ctt----ac-g--ag-t-a-gg-gc-ta-cac-acgtg-c--ta--caatg---g-cgta-t-a--c-aaa-ga-ga--------------------------------------------------------------------------------------------------a-g-c-g-a--a-ctcg-c--g---------------------------------------a-ga-g-c-----------a--a-g-cg---g----------a--cct-c------a-t-aaagt-ac-g-t-c-g-tag-tcc--------gga-t-tggag-tc--t-gcaa-ct-c-------------------------------------------------------------------------------------------------g-actcc-a-t-g-aa-g-tc-ggaat-cg-c-ta--g-ta-at-c-g-t----aga-tc-a-g--a------at--gct-ac-g-gt-g-aat-acgt-t-cccgggcct-tgta----cacaccg-ccc-gtc-----a---ca--cca-tg-gg-a--g---tgg-g-tt-gc-aaa--a-gaa------g--t-agg-ta-g-c-t-t-aa-c-c-------------------------------------------------------------t-tc-g------------------------------------------------------------------------------------------------------gg-a--gg-g--c---gc-tta--cc--act-t----t-gtg-at-tca------------------------t........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................."); + refSeqs[0]->setName("7000004131500404"); refSeqs[0]->setAligned(".........................................................................................................................................AT-TGAA-C-GC--TGG-C--G-GC-A-GG--C----C-T--AACACA-T-GC-A-AGT-CGA-G-CG----------G-CAG-CG-G----------------------------AAAG-A-AG----------------------------------------------------CTT-G---------------------------------------------------------------------------------ACTT-CTTT----------------G-CC--G--GC--G--AG-C-GG-C-GG-A--C-------------GGG-TGAGT-A--AT-GT-C-T-G-GG---G-A--T-CT-G--C-C-CGA--TG-G------------------------------------------------------------------A-GG----GGG-AT-AA-CTA-------------------------C-T-G-----------------------GAA-A---CGG-TAG-CTAA-TA---CC-G--C-AT-A----------A--------------------C-------------------------------------GT-C-----------------------------------------------------------------------------------------------------------------------G-CA-A--------------------------------------------------------------------------------------------------------------------------------------G-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAA--G-T-G-GG-----G--GA-C--C--------------------------------------------------------------------------------------------------------------------TTC-G----------------------------------------------------------------------------------------------------------------------G-G--CC-TC--A---C-A--------------C----C-A---T-CG-G---AT---G-A-----A-CCC-AGA--T-GGG--A------TT--A--G-CT-A----G---TAGG-T-G-GG-G-T----AAT-GG-C-T-C-ACCT--A-GG-C-G--A-CG-A------------TCC-C-T------AG-CT-G-G-TCT-G-AG----A--GG-AT--G-AC-C-AG-CCAC-A-CTGGA--A-C-TG-A-GA-C-AC-G-G-TCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TTGCA-C-AA-T-GG--GG-GA-A----A-C-CC-T-GA-TG-CA-GCCA-TGCC-G-CG-T---G-T-G--T--GA-A-G--A--A-G-G-CC-----TT-CG---------G-G-T-T-G-T--A---AA-G-CAC--------TT-TC-A-G--C-GGG----GA-A--G---AA-GGCG---TT-A-GC---GT--T--AA-C---A----G-----CG-C-TAT-CGA-TT-GA-CG-TT-A-C-CT-G-CA-G---------AA-----------GAAGC-ACC-GG-C-TAA---C--T-CCGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GG-AG-GGT-GCA-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GCGT-AC--G-CA-G-G-C-G------------G--T-CT-G-T-T-AA----G-T-C-A---G-ATG-TG-A-AA-TC--CC-CGG-G--------------------------------------------------------------------CT-T-AA-------------------------------------------------------------------------CC-T-G-GG-AA-C----T-G-C-A-T-T--------T--GA-A-A-C-T-G-GCA--G-G-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-A-G-A-G-T-C-----T-CG--TA-G-A------------G-GG-G-GG-T----AG--AATT-CCA-G-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAG-A-TC-T-GGA--GG-A-AT-A-CC-GG--T--G--GC-GAA-G--G-C---G----G--C-C-CCCTG------G-AC-GA--------------------------------------------------------------AG-A-C-T--GA--CG-----CT-CA-GG--T-A-CGA--AA-G-C--------------G-TGGG-GAG-C-A-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CA--C-G-CTG-T-AAA--C-GATG-TC--GA-TT---------T-GA--A--G-G-TT-G-TG-G--C--------------------------------------------------------------------------------------CTT-GA--------------------------------------------------------------------------------------------------------------------------------------------------G-C-T-GT--G-G-C-T-TT-C------GG--A----GC-TAA--CG-C-G-T--T--AA-AT--C----G-ACC-GCC-T-G-GG-GAG-TA---CGG-----C-C--G-C-A-A-GGT-T--AAA-ACTC-AAA---------TGAA-TTG-ACGGG-G-G-CCCG----C-A--C-A-A-GCG-GT-G--G--AG-CA-T--GT-GGT-TT-AATT-C-G-ATG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-TACTC-TT-G-AC-A-T-C--------------CAG-A-G-------------A-AC-T-T-G--GC--A-GA-G-A-T--G-C-C--T-T-G-G--T-G-----CC-------------------------------------T--TC-G------------------------------------------GG----A----G---CT-CTG---A--GA---------------------------------------------------C-A-G-G-T-GCTG-CA-TGG-CT--GTC-GTC-A-GC-TC---G-TG-TT-G--TGA-AA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-T-TA--TC--C-TTTG--T-T-G-C-C---AG-C-G--A--T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----T----C-G------------G----G---A-A--CT---------------C-A-A-A-G-GA-G--AC-T-G-CCG--G-T------------------------------------G-A---TAA----------------------------------A-C-C-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAGT-C---ATC-A-T-G-G-C-C-CTT----AC-G--AG-T-A-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-CGCA-T-A--C-AAA-GA-GA--------------------------------------------------------------------------------------------------A-G-C-G-A--T-CTCG-C--G---------------------------------------A-GA-G-T-----------C--A-G-CG---G----------A--CCT-C------A-C-AAAGT-GC-G-T-C-G-TAG-TCC--------GGA-T-TGGAG-TC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-ACTCC-A-T-G-AA-G-TC-GGAAT-CG-C-TA--G-TA-AT-C-G-T----GGA-TC-A-G--A------AT--GCC-AC-G-GT-G-AAT-ACGT-T-CCTGGGCCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-TG-GG-A--G---TGG-G-TT-GC-AAA--A-GAA------G--T-AGG-TA-G-C-T-T-AA-C-C-------------------------------------------------------------T-TC-G------------------------------------------------------------------------------------------------------GG-A--GG-G--C---GC-TTA--CC--ACT-T----T-GTG-AT-TCA------------------------TG--ACT-GGGG-TG-AAG-TCGTAACAA-GGTAA-CCGT-AGGGGAA-CCT......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................"); + for (int i = 0; i < refSeqs.size(); i++) { + string newAligned = ""; + for (int j = 0; j < refSeqs[i]->getAligned().length(); j++) { + newAligned += toupper(refSeqs[i]->getAligned()[j]); + } + refSeqs[i]->setAligned(newAligned); + }*/ for (int i = 0; i < refSeqs.size(); i++) { for (int j = i+1; j < refSeqs.size(); j++) { + if (m->control_pressed) { return "no"; } + //make copies of query and each parent because runBellerophon removes gaps and messes them up Sequence* q = new Sequence(query->getName(), query->getAligned()); Sequence* leftParent = new Sequence(refSeqs[i]->getName(), refSeqs[i]->getAligned()); Sequence* rightParent = new Sequence(refSeqs[j]->getName(), refSeqs[j]->getAligned()); + + map spots; //map from spot in original sequence to spot in filtered sequence for query and both parents + vector divs = runBellerophon(q, leftParent, rightParent, spots); + //cout << divs.size() << endl; + if (m->control_pressed) { + delete q; + delete leftParent; + delete rightParent; + return "no"; + } + +// cout << divs.size() << endl; + vector selectedDivs; + for (int k = 0; k < divs.size(); k++) { + + vector snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd); + vector snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd); + + if (m->control_pressed) { + delete q; + delete leftParent; + delete rightParent; + return "no"; + } + + int numSNPSLeft = snpsLeft.size(); + int numSNPSRight = snpsRight.size(); + + //require at least 3 SNPs on each side of the break +// if ((numSNPSLeft >= 3) && (numSNPSRight >= 3)) { + if ((numSNPSLeft >= 4) && (numSNPSRight >= 4)) { + + //removed in 12/09 version of chimeraSlayer + //int winSizeLeft = divs[k].winLEnd - divs[k].winLStart + 1; + //int winSizeRight = divs[k].winREnd - divs[k].winRStart + 1; + + //float snpRateLeft = numSNPSLeft / (float) winSizeLeft; + //float snpRateRight = numSNPSRight / (float) winSizeRight; + //float logR = log(snpRateLeft / snpRateRight) / log(2.0); + + // do not accept excess snp ratio on either side of the break + //if (abs(logR) < 1 ) { + + float BS_A, BS_B; + bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, iters); + + if (m->control_pressed) { + delete q; + delete leftParent; + delete rightParent; + return "no"; + } + + divs[k].bsa = BS_A; + divs[k].bsb = BS_B; + + divs[k].bsMax = max(BS_A, BS_B); + + divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra); + + //so results reflect orignal alignment + divs[k].winLStart = spots[divs[k].winLStart]; + divs[k].winLEnd = spots[divs[k].winLEnd]; + divs[k].winRStart = spots[divs[k].winRStart]; + divs[k].winREnd = spots[divs[k].winREnd]; + + selectedDivs.push_back(divs[k]); + //} + } + } - vector divs = runBellerophon(q, leftParent, rightParent); + //save selected + for (int m = 0; m < selectedDivs.size(); m++) { all.push_back(selectedDivs[m]); } delete q; delete leftParent; delete rightParent; } - } - + // compute bootstrap support + if (all.size() > 0) { + //sort them + sort(all.begin(), all.end(), compareDataStruct); + reverse(all.begin(), all.end()); + + outputResults = all; + return "yes"; + } + else { + outputResults = all; + return "no"; + } } catch(exception& e) { - errorOut(e, "Slayer", "getResults"); + m->errorOut(e, "Slayer", "getResults"); exit(1); } } /***********************************************************************/ -vector Slayer::runBellerophon(Sequence* query, Sequence* parentA, Sequence* parentB) { +vector Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* pB, map& spots) { try{ vector data; //vertical filter vector temp; - verticalFilter(temp); + temp.push_back(q); temp.push_back(pA); temp.push_back(pB); + + //maps spot in new alignment to spot in alignment before filter + spots = verticalFilter(temp); //fills baseSpots + + //get these to avoid numerous function calls + string query = q->getAligned(); + string parentA = pA->getAligned(); + string parentB = pB->getAligned(); + int length = query.length(); +/*cout << q->getName() << endl << q->getAligned() << endl << endl; +cout << pA->getName() << endl << pA->getAligned() << endl << endl; +cout << pB->getName() << endl << pB->getAligned() << endl << endl; +cout << " length = " << length << endl; +cout << q->getName() << endl; +cout << pA->getName() << '\t'; +cout << pB->getName() << endl;*/ + + //check window size + if (length < (2*windowSize+windowStep)) { +// m->mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); m->mothurOutEndLine(); + windowSize = length / 4; + } + + for (int i = windowSize-1; i <= (length - windowSize); i += windowStep) { - int alignLength = query->getAligned().length(); + if (m->control_pressed) { return data; } + int breakpoint = i; + int leftLength = breakpoint + 1; + int rightLength = length - leftLength; + + float QLA = computePercentID(query, parentA, 0, breakpoint); + float QRB = computePercentID(query, parentB, breakpoint+1, length - 1); + + float QLB = computePercentID(query, parentB, 0, breakpoint); + float QRA = computePercentID(query, parentA, breakpoint+1, length - 1); + + float LAB = computePercentID(parentA, parentB, 0, breakpoint); + float RAB = computePercentID(parentA, parentB, breakpoint+1, length - 1); + + float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length; + float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length; + float QB = ((QLB*leftLength) + (QRB*rightLength)) / (float) length; + + float QLA_QRB = ((QLA*leftLength) + (QRB*rightLength)) / (float) length; + float QLB_QRA = ((QLB*leftLength) + (QRA*rightLength)) / (float) length; + + //in original and not used + //float avgQA_QB = ((QA*leftLength) + (QB*rightLength)) / (float) length; + + float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB)); + float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB)); +//cout << leftLength << '\t' << rightLength << '\t' << QLA << '\t' << QRB << '\t' << QLB << '\t' << QRA << '\t' << LAB << '\t' << RAB << '\t' << AB << '\t' << QA << '\t' << QB << '\t' << QLA_QRB << '\t' << QLB_QRA << endl; + +//cout << divRThreshold << endl; +//cout << breakpoint << '\t' << divR_QLA_QRB << '\t' << divR_QLB_QRA << endl; + //is one of them above the + if (divR_QLA_QRB >= divRThreshold || divR_QLB_QRA >= divRThreshold) { + + if (((QLA_QRB > QA) && (QLA_QRB > QB) && (QLA >= parentFragmentThreshold) && (QRB >= parentFragmentThreshold)) || + ((QLB_QRA > QA) && (QLB_QRA > QB) && (QLB >=parentFragmentThreshold) && (QRA >= parentFragmentThreshold))) { + + data_struct member; + + member.divr_qla_qrb = divR_QLA_QRB; + member.divr_qlb_qra = divR_QLB_QRA; + member.qla_qrb = QLA_QRB; + member.qlb_qra = QLB_QRA; + member.qla = QLA; + member.qrb = QRB; + member.ab = AB; + member.qa = QA; + member.qb = QB; + member.lab = LAB; + member.rab = RAB; + member.qra = QRA; + member.qlb = QLB; + member.winLStart = 0; + member.winLEnd = breakpoint; + member.winRStart = breakpoint+1; + member.winREnd = length-1; + member.querySeq = *(q); + member.parentA = *(pA); + member.parentB = *(pB); + member.bsa = 0; + member.bsb = 0; + member.bsMax = 0; + member.chimeraMax = 0; + + data.push_back(member); + + }//if + }//if + }//for + return data; + } + catch(exception& e) { + m->errorOut(e, "Slayer", "runBellerophon"); + exit(1); + } +} +/***********************************************************************/ +vector Slayer::getSNPS(string parentA, string query, string parentB, int left, int right) { + try { + + vector data; +//cout << left << '\t' << right << endl; + for (int i = left; i <= right; i++) { + + char A = parentA[i]; + char Q = query[i]; + char B = parentB[i]; + + if ((A != Q) || (B != Q)) { +//cout << "not equal " << Q << '\t' << A << '\t' << B << endl; + + //ensure not neighboring a gap. change to 12/09 release of chimeraSlayer - not sure what this adds, but it eliminates alot of SNPS + if ( + //did query loose a base here during filter?? + ( i == 0 || abs (baseSpots[0][i] - baseSpots[0][i-1]) == 1) && + ( i == query.length() || abs (baseSpots[0][i] - baseSpots[0][i+1]) == 1) + && + //did parentA loose a base here during filter?? + ( i == 0 || abs (baseSpots[1][i] - baseSpots[1][i-1]) == 1) && + ( i == parentA.length() || abs (baseSpots[1][i] - baseSpots[1][i+1]) == 1) + && + //did parentB loose a base here during filter?? + ( i == 0 || abs (baseSpots[2][i] - baseSpots[2][i-1]) == 1) && + ( i == parentB.length() || abs (baseSpots[2][i] - baseSpots[2][i+1]) == 1) + ) + { + + snps member; + member.queryChar = Q; + member.parentAChar = A; + member.parentBChar = B; +//cout << "not neighboring a gap " << Q << '\t' << A << '\t' << B << '\t' << baseSpots[0][i] << '\t' << baseSpots[0][i+1] << '\t' << baseSpots[0][i-1] << '\t' << baseSpots[1][i] << '\t' << baseSpots[1][i+1] << '\t' << baseSpots[1][i-1] << '\t' << baseSpots[2][i] << '\t' << baseSpots[2][i+1] << '\t' << baseSpots[2][i-1] << endl; + data.push_back(member); + } + } +// cout << i << '\t' << data.size() << endl; + } return data; } catch(exception& e) { - errorOut(e, "Slayer", "runBellerophon"); + m->errorOut(e, "Slayer", "getSNPS"); + exit(1); + } +} +/***********************************************************************/ +int Slayer::bootstrapSNPS(vector left, vector right, float& BSA, float& BSB, int numIters) { + try { + + srand((unsigned)time( NULL )); + + int count_A = 0; // sceneario QLA,QRB supported + int count_B = 0; // sceneario QLB,QRA supported + + int numLeft = max(1, int(left.size() * percentSNPSample/(float)100 + 0.5)); + int numRight = max(1, int(right.size() * percentSNPSample/(float)100 + 0.5)); + + for (int i = 0; i < numIters; i++) { + //random sampling with replacement. + + if (m->control_pressed) { return 0; } + + vector selectedLeft; + + for (int j = 0; j < numLeft; j++) { + int index = int(rand() % left.size()); + selectedLeft.push_back(left[index]); + } + + vector selectedRight; + for (int j = 0; j < numRight; j++) { + int index = int(rand() % right.size()); + selectedRight.push_back(right[index]); + } + + /* A ------------------------------------------ + # QLA QRA + # Q ------------------------------------------ + # | + # | + # Q ------------------------------------------ + # QLB QRB + # B ------------------------------------------ */ + + + float QLA = snpQA(selectedLeft); + float QRA = snpQA(selectedRight); + + float QLB = snpQB(selectedLeft); + float QRB = snpQB(selectedRight); + + //in original - not used - not sure why? + //float ALB = snpAB(selectedLeft); + //float ARB = snpAB(selectedRight); + + if ((QLA > QLB) && (QRB > QRA)) { + count_A++; + } + + if ((QLB > QLA) && (QRA > QRB)) { + count_B++; + } + +//cout << "selected left snp: \n"; +//for (int j = 0; j < selectedLeft.size(); j++) { cout << selectedLeft[j].parentAChar; } +//cout << endl; +//for (int j = 0; j < selectedLeft.size(); j++) { cout << selectedLeft[j].queryChar; } +//cout << endl; +//for (int j = 0; j < selectedLeft.size(); j++) { cout << selectedLeft[j].parentBChar; } +//cout << endl; +//cout << "selected right snp: \n"; +//for (int j = 0; j < selectedRight.size(); j++) { cout << selectedRight[j].parentAChar; } +//cout << endl; +//for (int i = 0; i < selectedRight.size(); i++) { cout << selectedRight[i].queryChar; } +//cout << endl; +//for (int i = 0; i < selectedRight.size(); i++) { cout << selectedRight[i].parentBChar; } +//cout << endl; + } + + + + + BSA = (float) count_A / (float) iters * 100; + BSB = (float) count_B / (float) iters * 100; +//cout << "bsa = " << BSA << " bsb = " << BSB << endl; + + //run borderline bootstrap values longer + //if (numIters < 1000) { + //are you within 10 points of min bootstrap value cutoff + // if (((abs((double)(BSA - minBS))) <= 5) || ((abs((double)(BSB - minBS))) <= 5)) { + // m->mothurOut("extending bootstrap for " + myQuery.getName()); m->mothurOutEndLine(); + // bootstrapSNPS(left, right, BSA, BSB, 1000); + // } + //} + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "Slayer", "bootstrapSNPS"); + exit(1); + } +} +/***********************************************************************/ +float Slayer::snpQA(vector data) { + try { + + int numIdentical = 0; + + for (int i = 0; i < data.size(); i++) { + if (data[i].parentAChar == data[i].queryChar) { + numIdentical++; + } + } + + float percentID = (numIdentical / (float) data.size()) * 100; + + return percentID; + } + catch(exception& e) { + m->errorOut(e, "Slayer", "snpQA"); + exit(1); + } +} +/***********************************************************************/ +float Slayer::snpQB(vector data) { + try { + + int numIdentical = 0; + + for (int i = 0; i < data.size(); i++) { + if (data[i].parentBChar == data[i].queryChar) { + numIdentical++; + } + } + + float percentID = (numIdentical / (float) data.size()) * 100; + + return percentID; + + } + catch(exception& e) { + m->errorOut(e, "Slayer", "snpQB"); + exit(1); + } +} +/***********************************************************************/ +float Slayer::snpAB(vector data) { + try { + int numIdentical = 0; + + for (int i = 0; i < data.size(); i++) { + if (data[i].parentAChar == data[i].parentBChar) { + numIdentical++; + } + } + + float percentID = (numIdentical / (float) data.size()) * 100; + + return percentID; + + } + catch(exception& e) { + m->errorOut(e, "Slayer", "snpAB"); exit(1); } } @@ -69,7 +468,7 @@ float Slayer::computePercentID(string queryFrag, string parent, int left, int ri try { int total = 0; int matches = 0; - + for (int i = left; i <= right; i++) { total++; if (queryFrag[i] == parent[i]) { @@ -82,14 +481,18 @@ float Slayer::computePercentID(string queryFrag, string parent, int left, int ri return percentID; } catch(exception& e) { - errorOut(e, "Slayer", "computePercentID"); + m->errorOut(e, "Slayer", "computePercentID"); exit(1); } } /***********************************************************************/ -//this is a vertical filter -void Slayer::verticalFilter(vector seqs) { +//remove columns that contain any gaps +map Slayer::verticalFilter(vector seqs) { try { + //find baseSpots + baseSpots.clear(); + baseSpots.resize(3); //query, parentA, parentB + vector gaps; gaps.resize(seqs[0]->getAligned().length(), 0); string filterString = (string(seqs[0]->getAligned().length(), '1')); @@ -101,32 +504,50 @@ void Slayer::verticalFilter(vector seqs) { for (int j = 0; j < seqAligned.length(); j++) { //if this spot is a gap - if ((seqAligned[j] == '-') || (seqAligned[j] == '.')) { gaps[j]++; } + if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; } } } - //zero out spot where all sequences have blanks + //zero out spot where any sequences have blanks int numColRemoved = 0; + int count = 0; + map maskMap; maskMap.clear(); + for(int i = 0; i < seqs[0]->getAligned().length(); i++){ - if(gaps[i] == seqs.size()) { filterString[i] = '0'; numColRemoved++; } + if(gaps[i] != 0) { filterString[i] = '0'; numColRemoved++; } + else { + maskMap[count] = i; + count++; + } } - + //for each sequence for (int i = 0; i < seqs.size(); i++) { string seqAligned = seqs[i]->getAligned(); string newAligned = ""; + int baseCount = 0; + int count = 0; for (int j = 0; j < seqAligned.length(); j++) { + //are you a base + if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N')) { baseCount++; } + //if this spot is not a gap - if (filterString[j] == '1') { newAligned += seqAligned[j]; } + if (filterString[j] == '1') { + newAligned += seqAligned[j]; + baseSpots[i][count] = baseCount; + count++; + } } seqs[i]->setAligned(newAligned); } + + return maskMap; } catch(exception& e) { - errorOut(e, "Slayer", "verticalFilter"); + m->errorOut(e, "Slayer", "verticalFilter"); exit(1); } }