X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=preclustercommand.cpp;h=bd3f172c2bcaa3e13ced0b5c57d92e39c9073969;hp=0c7895cfd3c4b5c1988977f102d5523bfe20f9e0;hb=615301e57c25e241356a9c2380648d117709458d;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e diff --git a/preclustercommand.cpp b/preclustercommand.cpp index 0c7895c..bd3f172 100644 --- a/preclustercommand.cpp +++ b/preclustercommand.cpp @@ -17,8 +17,10 @@ vector PreClusterCommand::setParameters(){ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname); CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount); CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup); - CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pdiffs); + CommandParameter pdiffs("diffs", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pdiffs); CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + CommandParameter ptopdown("topdown", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptopdown); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); @@ -37,11 +39,12 @@ string PreClusterCommand::getHelpString(){ string helpString = ""; helpString += "The pre.cluster command groups sequences that are within a given number of base mismatches.\n"; helpString += "The pre.cluster command outputs a new fasta and name file.\n"; - helpString += "The pre.cluster command parameters are fasta, name, group, count, processors and diffs. The fasta parameter is required. \n"; + helpString += "The pre.cluster command parameters are fasta, name, group, count, topdown, processors and diffs. The fasta parameter is required. \n"; helpString += "The name parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n"; helpString += "The group parameter allows you to provide a group file so you can cluster by group. \n"; helpString += "The count parameter allows you to provide a count file so you can cluster by group. \n"; helpString += "The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n"; + helpString += "The topdown parameter allows you to specify whether to cluster from largest abundance to smallest or smallest to largest. Default=T, meaning largest to smallest.\n"; helpString += "The pre.cluster command should be in the following format: \n"; helpString += "pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n"; helpString += "Example pre.cluster(fasta=amazon.fasta, diffs=2).\n"; @@ -189,7 +192,7 @@ PreClusterCommand::PreClusterCommand(string option) { else if (countfile == "not open") { abort = true; countfile = ""; } else { m->setCountTableFile(countfile); - ct.readTable(countfile); + ct.readTable(countfile, true); if (ct.hasGroupInfo()) { bygroup = true; } else { bygroup = false; } } @@ -210,6 +213,9 @@ PreClusterCommand::PreClusterCommand(string option) { m->setProcessors(temp); m->mothurConvert(temp, processors); + temp = validParameter.validFile(parameters, "topdown", false); if(temp == "not found"){ temp = "T"; } + topdown = m->isTrue(temp); + if (countfile == "") { if (namefile == "") { vector files; files.push_back(fastafile); @@ -440,7 +446,7 @@ int PreClusterCommand::createProcessesGroups(string newFName, string newNName, s // Allocate memory for thread data. string extension = toString(i) + ".temp"; - preClusterData* tempPreCluster = new preClusterData(fastafile, namefile, groupfile, countfile, (newFName+extension), (newNName+extension), newMFile, groups, m, lines[i].start, lines[i].end, diffs, i); + preClusterData* tempPreCluster = new preClusterData(fastafile, namefile, groupfile, countfile, (newFName+extension), (newNName+extension), newMFile, groups, m, lines[i].start, lines[i].end, diffs, topdown, i); pDataArray.push_back(tempPreCluster); processIDS.push_back(i); @@ -458,6 +464,9 @@ int PreClusterCommand::createProcessesGroups(string newFName, string newNName, s //Close all thread handles and free memory allocations. for(int i=0; i < pDataArray.size(); i++){ + if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) { + m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true; + } for (int j = 0; j < pDataArray[i]->mapFileNames.size(); j++) { outputNames.push_back(pDataArray[i]->mapFileNames[j]); outputTypes["map"].push_back(pDataArray[i]->mapFileNames[j]); } @@ -545,52 +554,94 @@ int PreClusterCommand::process(string newMapFile){ m->openOutputFile(newMapFile, out); //sort seqs by number of identical seqs - sort(alignSeqs.begin(), alignSeqs.end(), comparePriority); + if (topdown) { sort(alignSeqs.begin(), alignSeqs.end(), comparePriorityTopDown); } + else { sort(alignSeqs.begin(), alignSeqs.end(), comparePriorityDownTop); } int count = 0; int numSeqs = alignSeqs.size(); - //think about running through twice... - for (int i = 0; i < numSeqs; i++) { - - //are you active - // itActive = active.find(alignSeqs[i].seq.getName()); - - if (alignSeqs[i].active) { //this sequence has not been merged yet - - string chunk = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n"; - - //try to merge it with all smaller seqs - for (int j = i+1; j < numSeqs; j++) { - - if (m->control_pressed) { out.close(); return 0; } - - if (alignSeqs[j].active) { //this sequence has not been merged yet - //are you within "diff" bases - int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned()); - - if (mismatch <= diffs) { - //merge - alignSeqs[i].names += ',' + alignSeqs[j].names; - alignSeqs[i].numIdentical += alignSeqs[j].numIdentical; - - chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n"; - - alignSeqs[j].active = 0; - alignSeqs[j].numIdentical = 0; - count++; - } - }//end if j active - }//end for loop j - - //remove from active list - alignSeqs[i].active = 0; - - out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;; - - }//end if active i - if(i % 100 == 0) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); } - } + if (topdown) { + //think about running through twice... + for (int i = 0; i < numSeqs; i++) { + + if (alignSeqs[i].active) { //this sequence has not been merged yet + + string chunk = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n"; + + //try to merge it with all smaller seqs + for (int j = i+1; j < numSeqs; j++) { + + if (m->control_pressed) { out.close(); return 0; } + + if (alignSeqs[j].active) { //this sequence has not been merged yet + //are you within "diff" bases + int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned()); + + if (mismatch <= diffs) { + //merge + alignSeqs[i].names += ',' + alignSeqs[j].names; + alignSeqs[i].numIdentical += alignSeqs[j].numIdentical; + + chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n"; + + alignSeqs[j].active = 0; + alignSeqs[j].numIdentical = 0; + count++; + } + }//end if j active + }//end for loop j + + //remove from active list + alignSeqs[i].active = 0; + + out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;; + + }//end if active i + if(i % 100 == 0) { m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); } + } + }else { + map mapFile; + map originalCount; + map::iterator itCount; + for (int i = 0; i < numSeqs; i++) { mapFile[i] = ""; originalCount[i] = alignSeqs[i].numIdentical; } + + //think about running through twice... + for (int i = 0; i < numSeqs; i++) { + + //try to merge it into larger seqs + for (int j = i+1; j < numSeqs; j++) { + + if (m->control_pressed) { out.close(); return 0; } + + if (originalCount[j] > originalCount[i]) { //this sequence is more abundant than I am + //are you within "diff" bases + int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned()); + + if (mismatch <= diffs) { + //merge + alignSeqs[j].names += ',' + alignSeqs[i].names; + alignSeqs[j].numIdentical += alignSeqs[i].numIdentical; + + mapFile[j] = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[i].seq.getAligned() + "\n" + mapFile[i]; + alignSeqs[i].numIdentical = 0; + originalCount.erase(i); + mapFile[i] = ""; + count++; + j+=numSeqs; //exit search, we merged this one in. + } + }//end abundance check + }//end for loop j + + if(i % 100 == 0) { m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); } + } + + for (int i = 0; i < numSeqs; i++) { + if (alignSeqs[i].numIdentical != 0) { + out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n" << mapFile[i] << endl; + } + } + + } out.close(); if(numSeqs % 100 != 0) { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); } @@ -851,13 +902,13 @@ void PreClusterCommand::readNameFile(){ while (!in.eof()) { in >> firstCol >> secondCol; m->gobble(in); + + m->checkName(firstCol); + m->checkName(secondCol); + int size = m->getNumNames(secondCol); + names[firstCol] = secondCol; - int size = 1; - - for(int i=0;i