From: westcott Date: Thu, 30 Jul 2009 19:08:54 +0000 (+0000) Subject: working on chimeras X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=fe346922fe0af5b1a025beacb211078d37598fd4 working on chimeras --- diff --git a/chimera.h b/chimera.h index 106d24c..9142bac 100644 --- a/chimera.h +++ b/chimera.h @@ -65,7 +65,7 @@ class Chimera { virtual void setMask(string filename) { try { - if (filename == "") { + if (filename == "default") { //default is from wigeon 236627 EU009184.1 Shigella dysenteriae str. FBD013 seqMask = ".....................................................................................................AAATTGAAGAGTTT-GA--T-CA-T-G-GCTC-AG-AT-TGAA-C-GC--TGG-C--G-GC-A-GG--C----C-T--AACACA-T-GC-A-AGT-CGA-A-CG----------G-TAA-CA-G----------------------------GAAG-A-AG----------------------------------------------------CTT-G----------------------------------------------------------------------------------CT-TCTTT----------------G-CT--G--AC--G--AG-T-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-----------------------------------------------------------------------------------------------------------------------G-CA-A--------------------------------------------------------------------------------------------------------------------------------------G-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAA--G-A-G-GG-----G--GA-C-CT--------------------------------------------------------------------------------------------------------------------TCG-G----------------------------------------------------------------------------------------------------------------------G----CC-TC--T---T-G--------------C----C-A---T-CG-G---AT---G-T-----G-CCC-AGA--T-GGG--A------TT--A--G-CT-A----G---TAGG-T-G-GG-G-T----AAC-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-A--T--GA-A-G--A--A-G-G-CC-----TT-CG---------G-G-T-T-G-T--A---AA-G-TAC--------TT-TC-A-G--C-GGG----GA-G--G---AA-GGGA---GTAA-AG----T--T--AA-T---A----C-----CT-T-TGC-TCA-TT-GA-CG-TT-A-C-CC-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-CGG-G--------------------------------------------------------------------CT-C-AA-------------------------------------------------------------------------CC-T-G-GG-AA-C----T-G-C-A-T-C--------T--GA-T-A-C-T-G-GCA--A-G-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-T-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-CT---------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-GT--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-TGGTC-TT-G-AC-A-T-C--------------CAC-G-G-------------A-AG-T-T-T--TC--A-GA-G-A-T--G-A-G--A-A-T-G--T-G-----CC-------------------------------------T--TC-G------------------------------------------GG----A----A---CC-GTG---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-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GG---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--AC-C-A-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-CGCA-T-A--C-AAA-GA-GA--------------------------------------------------------------------------------------------------A-G-C-G-A--C-CTCG-C--G---------------------------------------A-GA-G-C-----------A--A-G-CG---G----------A--CCT-C------A-T-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-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--------------------------------------------------------------TT----C-------------------------------------------------------------------------------------------------G--GG-A--GG-G--C---GC-TTA--CC--ACT-T----T-GTG-AT-TCA------------------------TG--ACT-GGGG-TG-AAG-TCGTAACAA-GGTAA-CCGT-AGGGGAA-CCTG-CGGT-TGGATCACCTCCTTA................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................"; }else{ diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp index ba980a5..17f3a71 100644 --- a/chimeraseqscommand.cpp +++ b/chimeraseqscommand.cpp @@ -52,9 +52,15 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){ if (quanfile == "not open") { abort = true; } else if (quanfile == "not found") { quanfile = ""; } - maskfile = validParameter.validFile(parameters, "mask", true); - if (maskfile == "not open") { abort = true; } - else if (maskfile == "not found") { maskfile = ""; } + maskfile = validParameter.validFile(parameters, "mask", false); + if (maskfile == "not found") { maskfile = ""; } + else if (maskfile != "default") { + ifstream in; + int ableToOpen = openInputFile(maskfile, in); + if (ableToOpen == 1) { abort = true; } + in.close(); + } + @@ -129,7 +135,7 @@ int ChimeraSeqsCommand::execute(){ if (quanfile != "") { chimera->setQuantiles(quanfile); } else { chimera->setQuantiles(""); } - if (maskfile == "") { mothurOut("You have not provided a mask, so I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); mothurOutEndLine(); } + if (maskfile == "default") { mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); mothurOutEndLine(); } chimera->setMask(maskfile); }else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0; } diff --git a/decalc.cpp b/decalc.cpp index 203482f..18377c2 100644 --- a/decalc.cpp +++ b/decalc.cpp @@ -14,13 +14,16 @@ void DeCalculator::setMask(string m) { try { seqMask = m; - //whereever there is a base in the mask, save that value is query and subject - for (int i = 0; i < seqMask.length(); i++) { - if (isalpha(seqMask[i])) { - h.insert(i); + if (seqMask.length() != 0) { + //whereever there is a base in the mask, save that value is query and subject + for (int i = 0; i < seqMask.length(); i++) { + if (isalpha(seqMask[i])) { + h.insert(i); + } } + }else { + for (int i = 0; i < alignLength; i++) { h.insert(i); } } - } catch(exception& e) { errorOut(e, "DeCalculator", "setMask"); @@ -94,7 +97,7 @@ vector DeCalculator::findWindows(Sequence* query, int front, int back, int size = (cutoff / 4); } - string seq = query->getAligned().substr(front, cutoff); + /* string seq = query->getAligned().substr(front, cutoff); //count bases int numBases = 0; @@ -129,9 +132,15 @@ vector DeCalculator::findWindows(Sequence* query, int front, int back, int //get last window if needed - if (totalBases < numBases) { win.push_back(back-size); cout << back-size << endl;} + if (totalBases < numBases) { win.push_back(back-size); } //cout << endl << endl; +*/ + //this follows wigeon, but we may want to consider that it chops off the end values if the sequence cannot be evenly divided into steps + for (int m = front; m < (back - size) ; m+=increment) { win.push_back(m); } + + + return win; } @@ -154,7 +163,7 @@ vector DeCalculator::calcObserved(Sequence* query, Sequence* subject, vec //cout << "start point = " << window[m] << " end point = " << window[m]+size << endl; int diff = 0; for (int b = 0; b < seqFrag.length(); b++) { - + if (seqFrag[b] != seqFragsub[b]) { diff++; } } @@ -178,6 +187,7 @@ float DeCalculator::calcDist(Sequence* query, Sequence* subject, int front, int //so you only look at the trimmed part of the sequence int cutoff = back - front; + int gaps = 0; //from first startpoint with length back-front string seqFrag = query->getAligned().substr(front, cutoff); @@ -185,11 +195,13 @@ float DeCalculator::calcDist(Sequence* query, Sequence* subject, int front, int int diff = 0; for (int b = 0; b < seqFrag.length(); b++) { + //ignore gaps + if((!isalpha(seqFrag[b])) && (!isalpha(seqFragsub[b]))) { gaps++; } if (seqFrag[b] != seqFragsub[b]) { diff++; } } //percentage of mismatched bases - float dist = diff / (float) seqFrag.length() * 100; + float dist = diff / (float) (seqFrag.length()-gaps) * 100; return dist; } @@ -317,12 +329,8 @@ vector DeCalculator::findQav(vector window, int size, vector //while you are in the window for this sequence int count = 0; for (int j = window[m]; j < (window[m]+size); j++) { - - //is this a spot that is included in the mask - if (h.count(j) > 0) { - average += probabilityProfile[j]; - count++; - } + average += probabilityProfile[j]; + count++; } average = average / count; @@ -408,17 +416,31 @@ void DeCalculator::removeObviousOutliers(vector< vector >& quantiles) { for (int i = 0; i < quantiles.size(); i++) { //find mean of this quantile score - float average = findAverage(quantiles[i]); + sort(quantiles[i].begin(), quantiles[i].end()); + float average = quantiles[i][int(quantiles[i].size() * 0.5)]; +cout << i << "\taverage = " << average << "\tquantiles[i].size = " << quantiles[i].size() << endl; vector newQuanI; //look at each value in quantiles to see if it is an outlier for (int j = 0; j < quantiles[i].size(); j++) { - float highCutoff, lowCutOff; + float highCutOff, lowCutOff; + //99% + highCutOff = sqrt(((quantiles[i][j] - average + 3) * (quantiles[i][j] - average + 3)) / (float)(quantiles[i].size() - 1)); - + //1% + lowCutOff = sqrt(((quantiles[i][j] - average - 3) * (quantiles[i][j] - average + 3)) / (float)(quantiles[i].size() - 1)); +//cout << "high = " << highCutOff << " low = " << lowCutOff << " de = " << quantiles[i][j] << endl; + //if this is below the highcutff and above the lowcutoff + if ((quantiles[i][j] < highCutOff) && (quantiles[i][j] > lowCutOff)) { + + newQuanI.push_back(quantiles[i][j]); + + }else { cout << "removed outlier: high = " << highCutOff << " low = " << lowCutOff << " de = " << quantiles[i][j] << endl; } } + + quantiles[i] = newQuanI; } @@ -452,17 +474,11 @@ float DeCalculator::getCoef(vector obs, vector qav) { try { //find average prob for this seqs windows - float probAverage = 0.0; - for (int j = 0; j < qav.size(); j++) { probAverage += qav[j]; } - probAverage = probAverage / (float) qav.size(); - + float probAverage = findAverage(qav); + //find observed average - float obsAverage = 0.0; - for (int j = 0; j < obs.size(); j++) { obsAverage += obs[j]; } - obsAverage = obsAverage / (float) obs.size(); -//cout << "sum ai / m = " << probAverage << endl; -//cout << "sum oi / m = " << obsAverage << endl; - + float obsAverage = findAverage(obs); + float coef = obsAverage / probAverage; return coef; diff --git a/decalc.h b/decalc.h index 1579d86..4ce45bf 100644 --- a/decalc.h +++ b/decalc.h @@ -28,7 +28,8 @@ class DeCalculator { ~DeCalculator() {}; set getPos() { return h; } - void setMask(string m); + void setMask(string); + void setAlignmentLength(int l) { alignLength = l; } void runMask(Sequence*); void trimSeqs(Sequence*, Sequence*, map&); void removeObviousOutliers(vector< vector >&); @@ -46,6 +47,7 @@ class DeCalculator { float findAverage(vector myVector); string seqMask; set h; + int alignLength; }; diff --git a/getseqscommand.cpp b/getseqscommand.cpp index 8406b81..509241d 100644 --- a/getseqscommand.cpp +++ b/getseqscommand.cpp @@ -285,7 +285,7 @@ void GetSeqsCommand::readGroup(){ //alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name void GetSeqsCommand::readAlign(){ try { - string outputFileName = getRootName(alignfile) + "pick" + getExtension(alignfile);; + string outputFileName = getRootName(getRootName(alignfile)) + "pick.align.report"; ofstream out; openOutputFile(outputFileName, out); diff --git a/pintail.cpp b/pintail.cpp index bca7df9..39ac13f 100644 --- a/pintail.cpp +++ b/pintail.cpp @@ -42,8 +42,8 @@ cout << "my quantile = " << quantiles[index][4] << endl; //is your DE value higher than the 95% string chimera; - if (DE[i] > quantiles[index][4]) { chimera = "Yes"; } - else { chimera = "No"; } + if (DE[i] > quantiles[index][4]) { chimera = "Yes"; } + else { chimera = "No"; } out << querySeqs[i]->getName() << '\t' << "div: " << deviation[i] << "\tstDev: " << DE[i] << "\tchimera flag: " << chimera << endl; if (chimera == "Yes") { @@ -126,6 +126,10 @@ void Pintail::getChimeras() { distcalculator = new ignoreGaps(); decalc = new DeCalculator(); + //if the user does enter a mask then you want to keep all the spots in the alignment + if (seqMask.length() == 0) { decalc->setAlignmentLength(querySeqs[0]->getAligned().length()); } + else { decalc->setAlignmentLength(seqMask.length()); } + decalc->setMask(seqMask); //find pairs @@ -163,7 +167,7 @@ void Pintail::getChimeras() { }else { probabilityProfile = readFreq(); } //make P into Q - for (int i = 0; i < probabilityProfile.size(); i++) { probabilityProfile[i] = 1 - probabilityProfile[i]; } //cout << i << '\t' << probabilityProfile[i] << endl; + for (int i = 0; i < probabilityProfile.size(); i++) { probabilityProfile[i] = 1 - probabilityProfile[i]; } //cout << i << '\t' << probabilityProfile[i] << endl; mothurOut("Done."); mothurOutEndLine(); //mask querys @@ -183,15 +187,15 @@ void Pintail::getChimeras() { if (processors == 1) { for (int j = 0; j < bestfit.size(); j++) { - cout << querySeqs[j]->getName() << " after mask = " << querySeqs[j]->getAligned() << endl << endl; - cout << bestfit[j]->getName() << " after mask = " << bestfit[j]->getAligned() << endl << endl; + //cout << querySeqs[j]->getName() << " after mask = " << querySeqs[j]->getAligned() << endl << endl; + ///cout << bestfit[j]->getName() << " after mask = " << bestfit[j]->getAligned() << endl << endl; decalc->trimSeqs(querySeqs[j], bestfit[j], trimmed[j]); } mothurOut("Finding window breaks... "); cout.flush(); for (int i = lines[0]->start; i < lines[0]->end; i++) { it = trimmed[i].begin(); -cout << i << '\t' << "trimmed = " << it->first << '\t' << it->second << endl; +//cout << querySeqs[i]->getName() << '\t' << "trimmed = " << it->first << '\t' << it->second << endl; vector win = decalc->findWindows(querySeqs[i], it->first, it->second, windowSizes[i], increment); windowsForeachQuery[i] = win; } @@ -204,13 +208,13 @@ cout << i << '\t' << "trimmed = " << it->first << '\t' << it->second << endl; mothurOut("Calculating observed distance... "); cout.flush(); for (int i = lines[0]->start; i < lines[0]->end; i++) { - cout << querySeqs[i]->getName() << '\t' << bestfit[i]->getName() << " windows = " << windowsForeachQuery[i].size() << " size = " << windowSizes[i] << endl; + //cout << querySeqs[i]->getName() << '\t' << bestfit[i]->getName() << " windows = " << windowsForeachQuery[i].size() << " size = " << windowSizes[i] << endl; vector obsi = decalc->calcObserved(querySeqs[i], bestfit[i], windowsForeachQuery[i], windowSizes[i]); for (int j = 0; j < obsi.size(); j++) { - cout << obsi[j] << '\t'; + //cout << obsi[j] << '\t'; } - cout << endl; + //cout << endl; obsDistance[i] = obsi; } mothurOut("Done."); mothurOutEndLine(); @@ -221,11 +225,11 @@ cout << i << '\t' << "trimmed = " << it->first << '\t' << it->second << endl; vector q = decalc->findQav(windowsForeachQuery[i], windowSizes[i], probabilityProfile); Qav[i] = q; -cout << i+1 << endl; +//cout << querySeqs[i]->getName() << endl; for (int j = 0; j < Qav[i].size(); j++) { - cout << Qav[i][j] << '\t'; + //cout << Qav[i][j] << '\t'; } -cout << endl << endl; +//cout << endl << endl; } mothurOut("Done."); mothurOutEndLine(); @@ -234,7 +238,7 @@ cout << endl << endl; mothurOut("Calculating alpha... "); cout.flush(); for (int i = lines[0]->start; i < lines[0]->end; i++) { float alpha = decalc->getCoef(obsDistance[i], Qav[i]); -cout << i+1 << "\tcoef = " << alpha << endl; +//cout << querySeqs[i]->getName() << "\tcoef = " << alpha << endl; seqCoef[i] = alpha; } mothurOut("Done."); mothurOutEndLine(); @@ -252,10 +256,10 @@ cout << i+1 << "\tcoef = " << alpha << endl; for (int i = lines[0]->start; i < lines[0]->end; i++) { float de = decalc->calcDE(obsDistance[i], expectedDistance[i]); DE[i] = de; -cout << querySeqs[i]->getName() << '\t' << "de value = " << de << endl; +//cout << querySeqs[i]->getName() << '\t' << "de value = " << de << endl; it = trimmed[i].begin(); float dist = decalc->calcDist(querySeqs[i], bestfit[i], it->first, it->second); -cout << querySeqs[i]->getName() << '\t' << "dist value = " << dist << endl; +//cout << querySeqs[i]->getName() << '\t' << "dist value = " << dist << endl; deviation[i] = dist; } mothurOut("Done."); mothurOutEndLine();