X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.cpp;h=67b2f31bebe6185fef4137d9c5e839a35b23f0b8;hb=ae57e166b2ed7b475ec3f466106bd76fabadd063;hp=3f6e0c975750d7e6bd69845a32e11e7e20b2b68a;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git diff --git a/preclustercommand.cpp b/preclustercommand.cpp index 3f6e0c9..67b2f31 100644 --- a/preclustercommand.cpp +++ b/preclustercommand.cpp @@ -8,6 +8,8 @@ */ #include "preclustercommand.h" +#include "sequenceparser.h" +#include "deconvolutecommand.h" //********************************************************************************************************************** inline bool comparePriority(seqPNode first, seqPNode second) { return (first.numIdentical > second.numIdentical); } @@ -17,7 +19,9 @@ vector PreClusterCommand::setParameters(){ try { CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup); CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs); + CommandParameter pbygroup("bygroup", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pbygroup); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); @@ -38,7 +42,9 @@ string PreClusterCommand::getHelpString(){ helpString += "The pre.cluster command outputs a new fasta and name file.\n"; helpString += "The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n"; helpString += "The names 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. \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 bygroup parameter allows you to indicate you whether you want to cluster sequences only within each group, default=T, when a groupfile is given. \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"; @@ -114,6 +120,14 @@ PreClusterCommand::PreClusterCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["name"] = inputDir + it->second; } } + + it = parameters.find("group"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["group"] = inputDir + it->second; } + } } //check for required parameters @@ -137,10 +151,25 @@ PreClusterCommand::PreClusterCommand(string option) { namefile = validParameter.validFile(parameters, "name", true); if (namefile == "not found") { namefile = ""; } else if (namefile == "not open") { abort = true; } - else { readNameFile(); m->setNameFile(namefile); } + else { m->setNameFile(namefile); } + + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not found") { groupfile = ""; } + else if (groupfile == "not open") { abort = true; groupfile = ""; } + else { m->setGroupFile(groupfile); } - string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; } + string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; } convert(temp, diffs); + + temp = validParameter.validFile(parameters, "bygroup", false); + if (temp == "not found") { + if (groupfile != "") { temp = "T"; } + else { temp = "F"; } + } + bygroup = m->isTrue(temp); + + if (bygroup && (groupfile == "")) { m->mothurOut("You cannot set bygroup=T, unless you provide a groupfile."); m->mothurOutEndLine(); abort=true; } + } } @@ -158,22 +187,133 @@ int PreClusterCommand::execute(){ int start = time(NULL); - //reads fasta file and return number of seqs - int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active + string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile)); + string newFastaFile = fileroot + "precluster" + m->getExtension(fastafile); + string newNamesFile = fileroot + "precluster.names"; - if (m->control_pressed) { return 0; } - - if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0; } - if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0; } + if (bygroup) { + //clear out old files + ofstream outFasta; m->openOutputFile(newFastaFile, outFasta); outFasta.close(); + ofstream outNames; m->openOutputFile(newNamesFile, outNames); outNames.close(); + + //parse fasta and name file by group + SequenceParser* parser; + if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile); } + else { parser = new SequenceParser(groupfile, fastafile); } + + vector groups = parser->getNamesOfGroups(); + + //precluster each group + for (int i = 0; i < groups.size(); i++) { + + start = time(NULL); + + if (m->control_pressed) { delete parser; m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; } + + m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine(); + + map thisNameMap; + if (namefile != "") { thisNameMap = parser->getNameMap(groups[i]); } + vector thisSeqs = parser->getSeqs(groups[i]); + + //fill alignSeqs with this groups info. + int numSeqs = loadSeqs(thisNameMap, thisSeqs); + + if (m->control_pressed) { delete parser; m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; } + + if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0; } + + int count = process(); + + if (m->control_pressed) { delete parser; m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; } + + m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine(); + m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); + printData(newFastaFile, newNamesFile); + + m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); + + } + + //run unique.seqs for deconvolute results + string inputString = "fasta=" + newFastaFile; + if (namefile != "") { inputString += ", name=" + newNamesFile; } + m->mothurOutEndLine(); + m->mothurOut("/******************************************/"); m->mothurOutEndLine(); + m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); + + Command* uniqueCommand = new DeconvoluteCommand(inputString); + uniqueCommand->execute(); + + map > filenames = uniqueCommand->getOutputFiles(); + + delete uniqueCommand; + + m->mothurOut("/******************************************/"); m->mothurOutEndLine(); + + newNamesFile = filenames["name"][0]; + newFastaFile = filenames["fasta"][0]; + + }else { + if (namefile != "") { readNameFile(); } + + //reads fasta file and return number of seqs + int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active - //clear sizes since you only needed this info to build the alignSeqs seqPNode structs -// sizes.clear(); + if (m->control_pressed) { return 0; } + if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0; } + if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0; } + + int count = process(); + + if (m->control_pressed) { return 0; } + + m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine(); + m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); + printData(newFastaFile, newNamesFile); + + m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); + } + + if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; } + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + m->mothurOut(newFastaFile); m->mothurOutEndLine(); outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile); + m->mothurOut(newNamesFile); m->mothurOutEndLine(); outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile); + m->mothurOutEndLine(); + + //set fasta file as new current fastafile + string current = ""; + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } + } + + itTypes = outputTypes.find("name"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); } + } + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "PreClusterCommand", "execute"); + exit(1); + } +} +/**************************************************************************************************/ +int PreClusterCommand::process(){ + try { + //sort seqs by number of identical seqs sort(alignSeqs.begin(), alignSeqs.end(), comparePriority); - + int count = 0; - + int numSeqs = alignSeqs.size(); + //think about running through twice... for (int i = 0; i < numSeqs; i++) { @@ -195,70 +335,32 @@ int PreClusterCommand::execute(){ //merge alignSeqs[i].names += ',' + alignSeqs[j].names; alignSeqs[i].numIdentical += alignSeqs[j].numIdentical; - + alignSeqs[j].active = 0; alignSeqs[j].numIdentical = 0; count++; } }//end if j active }//end if i != j - - //remove from active list + + //remove from active list alignSeqs[i].active = 0; }//end if active i if(i % 100 == 0) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); } } - if(numSeqs % 100 != 0) { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); } - - - string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile)); - - string newFastaFile = fileroot + "precluster" + m->getExtension(fastafile); - string newNamesFile = fileroot + "precluster.names"; - - if (m->control_pressed) { return 0; } - - m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine(); - m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine(); - printData(newFastaFile, newNamesFile); - - m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); - - if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; } - - m->mothurOutEndLine(); - m->mothurOut("Output File Names: "); m->mothurOutEndLine(); - m->mothurOut(newFastaFile); m->mothurOutEndLine(); outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile); - m->mothurOut(newNamesFile); m->mothurOutEndLine(); outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile); - m->mothurOutEndLine(); - - //set fasta file as new current fastafile - string current = ""; - itTypes = outputTypes.find("fasta"); - if (itTypes != outputTypes.end()) { - if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } - } - - itTypes = outputTypes.find("name"); - if (itTypes != outputTypes.end()) { - if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); } - } + if(numSeqs % 100 != 0) { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); } - return 0; + return count; } catch(exception& e) { - m->errorOut(e, "PreClusterCommand", "execute"); + m->errorOut(e, "PreClusterCommand", "process"); exit(1); } } - /**************************************************************************************************/ - -//this requires the names and fasta file to be in the same order - int PreClusterCommand::readFASTA(){ try { //ifstream inNames; @@ -313,7 +415,55 @@ int PreClusterCommand::readFASTA(){ exit(1); } } - +/**************************************************************************************************/ +int PreClusterCommand::loadSeqs(map& thisName, vector& thisSeqs){ + try { + length = 0; + alignSeqs.clear(); + map::iterator it; + bool error = false; + + for (int i = 0; i < thisSeqs.size(); i++) { + + if (m->control_pressed) { return 0; } + + if (namefile != "") { + it = thisName.find(thisSeqs[i].getName()); + + //should never be true since parser checks for this + if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; } + else{ + //get number of reps + int numReps = 0; + for(int j=0;j<(it->second).length();j++){ + if((it->second)[j] == ','){ numReps++; } + } + + seqPNode tempNode(numReps, thisSeqs[i], it->second); + alignSeqs.push_back(tempNode); + if (thisSeqs[i].getAligned().length() > length) { length = thisSeqs[i].getAligned().length(); } + } + }else { //no names file, you are identical to yourself + seqPNode tempNode(1, thisSeqs[i], thisSeqs[i].getName()); + alignSeqs.push_back(tempNode); + if (thisSeqs[i].getAligned().length() > length) { length = thisSeqs[i].getAligned().length(); } + } + } + + //sanity check + if (error) { m->control_pressed = true; } + + thisSeqs.clear(); + + return alignSeqs.size(); + } + + catch(exception& e) { + m->errorOut(e, "PreClusterCommand", "loadSeqs"); + exit(1); + } +} + /**************************************************************************************************/ int PreClusterCommand::calcMisMatches(string seq1, string seq2){ @@ -341,10 +491,14 @@ void PreClusterCommand::printData(string newfasta, string newname){ ofstream outFasta; ofstream outNames; - m->openOutputFile(newfasta, outFasta); - m->openOutputFile(newname, outNames); + if (bygroup) { + m->openOutputFileAppend(newfasta, outFasta); + m->openOutputFileAppend(newname, outNames); + }else { + m->openOutputFile(newfasta, outFasta); + m->openOutputFile(newname, outNames); + } - for (int i = 0; i < alignSeqs.size(); i++) { if (alignSeqs[i].numIdentical != 0) { alignSeqs[i].seq.printSequence(outFasta);