X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=preclustercommand.cpp;h=9f96ebd43a836bf699aa5ae1fff55f8752ad748a;hb=92de7f976371d41441ad41f02ca83af8b43cef5c;hp=1697ff7a0d57534b81e9b1f135cf494ae55c2d34;hpb=6777912b79eb6d011163da47f3ada09d1a9293c1;p=mothur.git diff --git a/preclustercommand.cpp b/preclustercommand.cpp index 1697ff7..9f96ebd 100644 --- a/preclustercommand.cpp +++ b/preclustercommand.cpp @@ -11,19 +11,71 @@ //********************************************************************************************************************** inline bool comparePriority(seqPNode first, seqPNode second) { return (first.numIdentical > second.numIdentical); } + //********************************************************************************************************************** +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 pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "PreClusterCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string PreClusterCommand::getHelpString(){ + try { + 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, 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 diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\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"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "PreClusterCommand", "getHelpString"); + exit(1); + } +} -PreClusterCommand::PreClusterCommand(string option){ +//********************************************************************************************************************** +PreClusterCommand::PreClusterCommand(){ try { - abort = false; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "PreClusterCommand", "PreClusterCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +PreClusterCommand::PreClusterCommand(string option) { + try { + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { - //valid paramters for this command - string Array[] = {"fasta", "name", "diffs", "outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -36,6 +88,11 @@ PreClusterCommand::PreClusterCommand(string option){ if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["name"] = tempOutNames; + //if the user changes the input directory command factory will send this info to us in the output parameter string inputDir = validParameter.validFile(parameters, "inputdir", false); if (inputDir == "not found"){ inputDir = ""; } @@ -44,7 +101,7 @@ PreClusterCommand::PreClusterCommand(string option){ it = parameters.find("fasta"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["fasta"] = inputDir + it->second; } } @@ -52,7 +109,7 @@ PreClusterCommand::PreClusterCommand(string option){ it = parameters.find("name"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["name"] = inputDir + it->second; } } @@ -60,13 +117,17 @@ PreClusterCommand::PreClusterCommand(string option){ //check for required parameters fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not found") { mothurOut("fasta is a required parameter for the pre.cluster command."); mothurOutEndLine(); abort = true; } + if (fastafile == "not found") { + fastafile = m->getFastaFile(); + if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; } + } else if (fastafile == "not open") { abort = true; } //if the user changes the output directory command factory will send this info to us in the output parameter outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; - outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it + outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it } //check for optional parameter and set defaults @@ -74,7 +135,7 @@ PreClusterCommand::PreClusterCommand(string option){ namefile = validParameter.validFile(parameters, "name", true); if (namefile == "not found") { namefile = ""; } else if (namefile == "not open") { abort = true; } -// else { readNameFile(); } + else { readNameFile(); } string temp = validParameter.validFile(parameters, "diffs", false); if(temp == "not found"){ temp = "1"; } convert(temp, diffs); @@ -82,29 +143,7 @@ PreClusterCommand::PreClusterCommand(string option){ } catch(exception& e) { - errorOut(e, "PreClusterCommand", "PreClusterCommand"); - exit(1); - } -} - -//********************************************************************************************************************** -PreClusterCommand::~PreClusterCommand(){} -//********************************************************************************************************************** - -void PreClusterCommand::help(){ - try { - mothurOut("The pre.cluster command groups sequences that are within a given number of base mismatches.\n"); - mothurOut("The pre.cluster command outputs a new fasta and name file.\n"); - mothurOut("The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n"); - mothurOut("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"); - mothurOut("The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n"); - mothurOut("The pre.cluster command should be in the following format: \n"); - mothurOut("pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n"); - mothurOut("Example pre.cluster(fasta=amazon.fasta, diffs=2).\n"); - mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); - } - catch(exception& e) { - errorOut(e, "PreClusterCommand", "help"); + m->errorOut(e, "PreClusterCommand", "PreClusterCommand"); exit(1); } } @@ -113,13 +152,17 @@ void PreClusterCommand::help(){ int PreClusterCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + int start = time(NULL); //reads fasta file and return number of seqs - int numSeqs = readNamesFASTA(); //fills alignSeqs and makes all seqs active + int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active + + if (m->control_pressed) { return 0; } - if (numSeqs == 0) { mothurOut("Error reading fasta file...please correct."); mothurOutEndLine(); return 0; } - if (diffs > length) { mothurOut("Error: diffs is greater than your sequence length."); mothurOutEndLine(); 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; } //clear sizes since you only needed this info to build the alignSeqs seqPNode structs // sizes.clear(); @@ -139,6 +182,9 @@ int PreClusterCommand::execute(){ //try to merge it with all smaller seqs for (int j = i+1; j < numSeqs; j++) { + + if (m->control_pressed) { 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()); @@ -157,103 +203,111 @@ int PreClusterCommand::execute(){ //remove from active list alignSeqs[i].active = 0; + }//end if active i - if(i % 100 == 0) { cout << i << '\t' << numSeqs - count << '\t' << count << endl; } + if(i % 100 == 0) { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); } } - string fileroot = outputDir + getRootName(getSimpleName(fastafile)); + 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" + getExtension(fastafile); + string newFastaFile = fileroot + "precluster" + m->getExtension(fastafile); string newNamesFile = fileroot + "precluster.names"; + if (m->control_pressed) { return 0; } - mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); mothurOutEndLine(); - mothurOut("pre.cluster removed " + toString(count) + " sequences."); mothurOutEndLine(); + 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) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); 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) { - errorOut(e, "PreClusterCommand", "execute"); + m->errorOut(e, "PreClusterCommand", "execute"); exit(1); } } + /**************************************************************************************************/ + +//this requires the names and fasta file to be in the same order + int PreClusterCommand::readFASTA(){ try { -// ifstream inFasta; -// openInputFile(fastafile, inFasta); -// length = 0; -//// map::iterator it; -// -// while (!inFasta.eof()) { -// Sequence temp(inFasta); //read seq -// -// if (temp.getName() != "") { -// if (namefile != "") { -// //make sure fasta and name files match -// it = names.find(temp.getName()); -// if (it == names.end()) { mothurOut(temp.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); } -// }else { sizes[temp.getName()] = 1; } -// -// seqPNode tempNode(sizes[temp.getName()], temp); -// alignSeqs.push_back(tempNode); -// active[temp.getName()] = true; -// } -// gobble(inFasta); -// } -// inFasta.close(); -// -// if (alignSeqs.size() != 0) { length = alignSeqs[0].seq.getAligned().length(); } -// - return alignSeqs.size(); - } - catch(exception& e) { - errorOut(e, "PreClusterCommand", "readFASTA"); - exit(1); - } -} -/**************************************************************************************************/ -//this seems to require the names and fasta file to be in the same order??? -int PreClusterCommand::readNamesFASTA(){ - try { - ifstream inNames; + //ifstream inNames; ifstream inFasta; - openInputFile(namefile, inNames); - openInputFile(fastafile, inFasta); + //m->openInputFile(namefile, inNames); + m->openInputFile(fastafile, inFasta); - string firstCol, secondCol, nameString; + //string firstCol, secondCol, nameString; length = 0; - while (inFasta && inNames) { - - inNames >> firstCol >> secondCol; - nameString = secondCol; + while (!inFasta.eof()) { - gobble(inNames); - int size = 1; - while (secondCol.find_first_of(',') != -1) { - size++; - secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length()); - } + if (m->control_pressed) { inFasta.close(); return 0; } + + //inNames >> firstCol >> secondCol; + //nameString = secondCol; + + //m->gobble(inNames); + //int size = 1; + //while (secondCol.find_first_of(',') != -1) { + // size++; + // secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length()); + //} + + Sequence seq(inFasta); m->gobble(inFasta); - Sequence seq(inFasta); gobble(inFasta); - if (seq.getName() != firstCol) { mothurOut(seq.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); } - else{ - seqPNode tempNode(size, seq, nameString); - alignSeqs.push_back(tempNode); - if (seq.getAligned().length() > length) { length = alignSeqs[0].seq.getAligned().length(); } - } + if (seq.getName() != "") { //can get "" if commented line is at end of fasta file + if (namefile != "") { + itSize = sizes.find(seq.getName()); + + if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); } + else{ + seqPNode tempNode(itSize->second, seq, names[seq.getName()]); + alignSeqs.push_back(tempNode); + if (seq.getAligned().length() > length) { length = seq.getAligned().length(); } + } + }else { //no names file, you are identical to yourself + seqPNode tempNode(1, seq, seq.getName()); + alignSeqs.push_back(tempNode); + if (seq.getAligned().length() > length) { length = seq.getAligned().length(); } + } + } } inFasta.close(); - inNames.close(); + //inNames.close(); return alignSeqs.size(); } catch(exception& e) { - errorOut(e, "PreClusterCommand", "readNamesFASTA"); + m->errorOut(e, "PreClusterCommand", "readFASTA"); exit(1); } } @@ -273,7 +327,7 @@ int PreClusterCommand::calcMisMatches(string seq1, string seq2){ return numBad; } catch(exception& e) { - errorOut(e, "PreClusterCommand", "calcMisMatches"); + m->errorOut(e, "PreClusterCommand", "calcMisMatches"); exit(1); } } @@ -285,8 +339,8 @@ void PreClusterCommand::printData(string newfasta, string newname){ ofstream outFasta; ofstream outNames; - openOutputFile(newfasta, outFasta); - openOutputFile(newname, outNames); + m->openOutputFile(newfasta, outFasta); + m->openOutputFile(newname, outNames); for (int i = 0; i < alignSeqs.size(); i++) { @@ -301,7 +355,32 @@ void PreClusterCommand::printData(string newfasta, string newname){ } catch(exception& e) { - errorOut(e, "PreClusterCommand", "printData"); + m->errorOut(e, "PreClusterCommand", "printData"); + exit(1); + } +} +/**************************************************************************************************/ + +void PreClusterCommand::readNameFile(){ + try { + ifstream in; + m->openInputFile(namefile, in); + string firstCol, secondCol; + + while (!in.eof()) { + in >> firstCol >> secondCol; m->gobble(in); + names[firstCol] = secondCol; + int size = 1; + + for(int i=0;ierrorOut(e, "PreClusterCommand", "readNameFile"); exit(1); } }