X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=slayer.cpp;h=a787f2727dd8290b89bffeb382bae6c15001110d;hp=9e5a61eaccfe04fdb079e105939bdb7d5be560a1;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=8c1196586860f830fc9c813f2a79abab7434dc4b diff --git a/slayer.cpp b/slayer.cpp index 9e5a61e..a787f27 100644 --- a/slayer.cpp +++ b/slayer.cpp @@ -13,23 +13,11 @@ 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(); } /***********************************************************************/ -string 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); - }*/ - + myQuery = query; + for (int i = 0; i < refSeqs.size(); i++) { for (int j = i+1; j < refSeqs.size(); j++) { @@ -37,99 +25,85 @@ string Slayer::getResults(Sequence* query, vector refSeqs) { 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()); - + Sequence q(query.getName(), query.getAligned()); + Sequence leftParent(refSeqs[i].getName(), refSeqs[i].getAligned()); + Sequence rightParent(refSeqs[j].getName(), refSeqs[j].getAligned()); + + //cout << q->getName() << endl << q->getAligned() << endl << endl; + //cout << leftParent.getName() << '\t' << leftParent.getAligned().length() << endl << endl; + //cout << rightParent.getName() << '\t' << rightParent.getAligned().length() << endl << endl; + //cout << q.getName() << '\t' << q.getAligned().length() << endl << endl; + //cout << rightParent->getName() << endl << rightParent->getAligned() << endl << endl; + //cout << " length = " << rightParent->getAligned().length() << endl; + 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; + + if (m->control_pressed) { return "no"; } +// cout << "examining:\t" << refSeqs[i]->getName() << '\t' << refSeqs[j]->getName() << 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"; - } + + if (m->control_pressed) { 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)) { +// cout << numSNPSLeft << '\t' << numSNPSRight << endl; + //require at least 4 SNPs on each side of the break 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"; - } + float BS_A, BS_B; + bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, iters); + + if (m->control_pressed) { return "no"; } - divs[k].bsa = BS_A; - divs[k].bsb = BS_B; + 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); - 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]; + //are we within 10 points of the bootstrap cutoff? +// if ((divs[k].bsMax >= (minBS-10)) && (iters < 1000)) { +// bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000); +// +// 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); +// } - selectedDivs.push_back(divs[k]); - //} + //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]); } } - + //save selected - for (int m = 0; m < selectedDivs.size(); m++) { all.push_back(selectedDivs[m]); } - - delete q; - delete leftParent; - delete rightParent; + for (int mi = 0; mi < selectedDivs.size(); mi++) { all.push_back(selectedDivs[mi]); } } } + // 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 { + }else { outputResults = all; return "no"; } @@ -140,30 +114,28 @@ string Slayer::getResults(Sequence* query, vector refSeqs) { } } /***********************************************************************/ -vector Slayer::runBellerophon(Sequence* q, Sequence* pA, Sequence* pB, map& spots) { +vector Slayer::runBellerophon(Sequence q, Sequence pA, Sequence pB, map& spots) { try{ vector data; //vertical filter - vector temp; - temp.push_back(q); temp.push_back(pA); temp.push_back(pB); + //cout << q.getName() << endl << q.getAligned() << endl << endl; + //cout << pA.getName() << endl << pA.getUnaligned() << endl << endl; + //cout << pB.getName() << endl << pB.getUnaligned() << endl << endl; //maps spot in new alignment to spot in alignment before filter - spots = verticalFilter(temp); //fills baseSpots + spots = verticalFilter(q, pA, pB); //fills baseSpots //get these to avoid numerous function calls - string query = q->getAligned(); - string parentA = pA->getAligned(); - string parentB = pB->getAligned(); + 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;*/ +//cout << q.getName() << endl << q.getAligned() << endl << endl; +//cout << pA.getName() << endl << pA.getUnaligned() << endl << endl; +//cout << pB.getName() << endl << pB.getUnaligned() << endl << endl; +//cout << " length = " << length << endl; //check window size if (length < (2*windowSize+windowStep)) { @@ -178,16 +150,16 @@ cout << pB->getName() << endl;*/ 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 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 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 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; @@ -200,6 +172,13 @@ cout << pB->getName() << endl;*/ float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB)); float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB)); + + + //cout << q->getName() << '\t'; + //cout << pA->getName() << '\t'; + //cout << pB->getName() << '\t'; + //cout << "bp: " << breakpoint << " CHIM_TYPE_A\t" << divR_QLA_QRB << "\tQLA: " << QLA << "\tQRB: " << QRB << "\tQLA_QRB: " << QLA_QRB; + //cout << "\tCHIM_TYPE_B\t" << divR_QLB_QRA << "\tQLB: " << QLB << "\tQRA: " << QRA << "\tQLB_QRA: " << QLB_QRA << endl; //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; @@ -229,9 +208,9 @@ cout << pB->getName() << endl;*/ member.winLEnd = breakpoint; member.winRStart = breakpoint+1; member.winREnd = length-1; - member.querySeq = *(q); - member.parentA = *(pA); - member.parentB = *(pB); + member.querySeq = q; + member.parentA = pA; + member.parentB = pB; member.bsa = 0; member.bsb = 0; member.bsMax = 0; @@ -243,6 +222,7 @@ cout << pB->getName() << endl;*/ }//if }//for + return data; } @@ -256,7 +236,7 @@ vector Slayer::getSNPS(string parentA, string query, string parentB, int l try { vector data; -//cout << left << '\t' << right << endl; + for (int i = left; i <= right; i++) { char A = parentA[i]; @@ -264,33 +244,31 @@ vector Slayer::getSNPS(string parentA, string query, string parentB, int l 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) + ( i == query.length()-1 || 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) + ( i == parentA.length()-1 || 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) + ( i == parentB.length()-1 || 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; @@ -376,20 +354,11 @@ int Slayer::bootstrapSNPS(vector left, vector right, float& BSA, flo } + //cout << count_A << '\t' << count_B << endl; - - BSA = (float) count_A / (float) iters * 100; - BSB = (float) count_B / (float) iters * 100; + BSA = (float) count_A / (float) numIters * 100; + BSB = (float) count_B / (float) numIters * 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; @@ -464,21 +433,42 @@ float Slayer::snpAB(vector data) { } } /***********************************************************************/ -float Slayer::computePercentID(string queryFrag, string parent, int left, int right) { +float Slayer::computePercentID(string queryAlign, string chimera, int left, int right) { try { - int total = 0; - int matches = 0; - + + int numIdentical = 0; + int countA = 0; + int countB = 0; for (int i = left; i <= right; i++) { - total++; - if (queryFrag[i] == parent[i]) { - matches++; + if (((queryAlign[i] != 'G') && (queryAlign[i] != 'T') && (queryAlign[i] != 'A') && (queryAlign[i] != 'C')&& (queryAlign[i] != '.') && (queryAlign[i] != '-')) || + ((chimera[i] != 'G') && (chimera[i] != 'T') && (chimera[i] != 'A') && (chimera[i] != 'C')&& (chimera[i] != '.') && (chimera[i] != '-'))) {} + else { + + bool charA = false; bool charB = false; + if ((queryAlign[i] == 'G') || (queryAlign[i] == 'T') || (queryAlign[i] == 'A') || (queryAlign[i] == 'C')) { charA = true; } + if ((chimera[i] == 'G') || (chimera[i] == 'T') || (chimera[i] == 'A') || (chimera[i] == 'C')) { charB = true; } + + if (charA || charB) { + + if (charA) { countA++; } + if (charB) { countB++; } + + if (queryAlign[i] == chimera[i]) { + numIdentical++; + } + } } + } + + float numBases = (countA + countB) /(float) 2; + + if (numBases == 0) { return 0; } + + float percentIdentical = (numIdentical/(float)numBases) * 100; - float percentID =( matches/(float)total) * 100; + return percentIdentical; - return percentID; } catch(exception& e) { m->errorOut(e, "Slayer", "computePercentID"); @@ -487,33 +477,41 @@ float Slayer::computePercentID(string queryFrag, string parent, int left, int ri } /***********************************************************************/ //remove columns that contain any gaps -map Slayer::verticalFilter(vector seqs) { +map Slayer::verticalFilter(Sequence& q, Sequence& pA, Sequence& pB) { try { //find baseSpots baseSpots.clear(); baseSpots.resize(3); //query, parentA, parentB - vector gaps; gaps.resize(seqs[0]->getAligned().length(), 0); + vector gaps; gaps.resize(q.getAligned().length(), 0); - string filterString = (string(seqs[0]->getAligned().length(), '1')); + string filterString = (string(q.getAligned().length(), '1')); - //for each sequence - for (int i = 0; i < seqs.size(); i++) { + string seqAligned = q.getAligned(); + for (int j = 0; j < seqAligned.length(); j++) { + //if this spot is a gap + if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; } + } - string seqAligned = seqs[i]->getAligned(); - - for (int j = 0; j < seqAligned.length(); j++) { - //if this spot is a gap - if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; } - } + seqAligned = pA.getAligned(); + for (int j = 0; j < seqAligned.length(); j++) { + //if this spot is a gap + if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; } + } + + seqAligned = pB.getAligned(); + for (int j = 0; j < seqAligned.length(); j++) { + //if this spot is a gap + if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N')) { gaps[j]++; } } + //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++){ + for(int i = 0; i < q.getAligned().length(); i++){ if(gaps[i] != 0) { filterString[i] = '0'; numColRemoved++; } else { maskMap[count] = i; @@ -521,29 +519,64 @@ map Slayer::verticalFilter(vector seqs) { } } - //for each sequence - for (int i = 0; i < seqs.size(); i++) { - - string seqAligned = seqs[i]->getAligned(); - string newAligned = ""; + seqAligned = q.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++; } + int baseCount = 0; + 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]; - baseSpots[i][count] = baseCount; - count++; - } + //if this spot is not a gap + if (filterString[j] == '1') { + newAligned += seqAligned[j]; + baseSpots[0][count] = baseCount; + count++; + } + } + + q.setAligned(newAligned); + + seqAligned = pA.getAligned(); + newAligned = ""; + + baseCount = 0; + 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]; + baseSpots[1][count] = baseCount; + count++; } + } + + pA.setAligned(newAligned); + + seqAligned = pB.getAligned(); + newAligned = ""; + + baseCount = 0; + count = 0; + for (int j = 0; j < seqAligned.length(); j++) { + //are you a base + if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N')) { baseCount++; } - seqs[i]->setAligned(newAligned); + //if this spot is not a gap + if (filterString[j] == '1') { + newAligned += seqAligned[j]; + baseSpots[2][count] = baseCount; + count++; + } } + pB.setAligned(newAligned); + + return maskMap; } catch(exception& e) {