X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sortseqscommand.cpp;fp=sortseqscommand.cpp;h=2c9e85404c86380232e96d3fb0fa9387ffef6a86;hb=731d19a6eaf81768ed35e4be25fbac5686a2a7a0;hp=1cc142f041e5ad4b9e7e21d5d53cec57c48724ad;hpb=6f6cc4061459b264b0933111d90674ad7e4b0ecb;p=mothur.git diff --git a/sortseqscommand.cpp b/sortseqscommand.cpp index 1cc142f..2c9e854 100644 --- a/sortseqscommand.cpp +++ b/sortseqscommand.cpp @@ -14,6 +14,7 @@ vector SortSeqsCommand::setParameters(){ try { CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta); + CommandParameter pflow("flow", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pflow); CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname); CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pgroup); CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy); @@ -36,8 +37,8 @@ vector SortSeqsCommand::setParameters(){ string SortSeqsCommand::getHelpString(){ try { string helpString = ""; - helpString += "The sort.seqs command puts the sequences in the same order for the following file types: accnos fasta, name, group, taxonomy or quality file.\n"; - helpString += "The sort.seqs command parameters are accnos, fasta, name, group, taxonomy, qfile and large.\n"; + helpString += "The sort.seqs command puts the sequences in the same order for the following file types: accnos fasta, name, group, taxonomy, flow or quality file.\n"; + helpString += "The sort.seqs command parameters are accnos, fasta, name, group, taxonomy, flow, qfile and large.\n"; helpString += "The accnos file allows you to specify the order you want the files in. If none is provided, mothur will use the order of the first file it reads.\n"; helpString += "The large parameters is used to indicate your files are too large to fit in RAM.\n"; helpString += "The sort.seqs command should be in the following format: sort.seqs(fasta=yourFasta).\n"; @@ -63,6 +64,7 @@ SortSeqsCommand::SortSeqsCommand(){ outputTypes["name"] = tempOutNames; outputTypes["group"] = tempOutNames; outputTypes["qfile"] = tempOutNames; + outputTypes["flow"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "SortSeqsCommand", "SortSeqsCommand"); @@ -99,6 +101,7 @@ SortSeqsCommand::SortSeqsCommand(string option) { outputTypes["name"] = tempOutNames; outputTypes["group"] = tempOutNames; outputTypes["qfile"] = tempOutNames; + outputTypes["flow"] = tempOutNames; //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 = ""; } @@ -155,6 +158,14 @@ SortSeqsCommand::SortSeqsCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["accnos"] = inputDir + it->second; } } + + it = parameters.find("flow"); + //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["flow"] = inputDir + it->second; } + } } @@ -169,6 +180,11 @@ SortSeqsCommand::SortSeqsCommand(string option) { else if (fastafile == "not found") { fastafile = ""; } else { m->setFastaFile(fastafile); } + flowfile = validParameter.validFile(parameters, "flow", true); + if (flowfile == "not open") { flowfile = ""; abort = true; } + else if (flowfile == "not found") { flowfile = ""; } + else { m->setFlowFile(flowfile); } + namefile = validParameter.validFile(parameters, "name", true); if (namefile == "not open") { namefile = ""; abort = true; } else if (namefile == "not found") { namefile = ""; } @@ -192,7 +208,7 @@ SortSeqsCommand::SortSeqsCommand(string option) { string temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "f"; } large = m->isTrue(temp); - if ((fastafile == "") && (namefile == "") && (groupfile == "") && (taxfile == "") && (qualfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy or quality."); m->mothurOutEndLine(); abort = true; } + if ((fastafile == "") && (namefile == "") && (groupfile == "") && (taxfile == "") && (flowfile == "") && (qualfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, group, taxonomy, flow or quality."); m->mothurOutEndLine(); abort = true; } if ((fastafile != "") && (namefile == "")) { vector files; files.push_back(fastafile); @@ -216,6 +232,7 @@ int SortSeqsCommand::execute(){ //read through the correct file and output lines you want to keep if (accnosfile != "") { readAccnos(); } if (fastafile != "") { readFasta(); } + if (flowfile != "") { readFlow(); } if (qualfile != "") { readQual(); } if (namefile != "") { readName(); } if (groupfile != "") { readGroup(); } @@ -255,7 +272,12 @@ int SortSeqsCommand::execute(){ itTypes = outputTypes.find("qfile"); if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); } - } + } + + itTypes = outputTypes.find("flow"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFlowFile(current); } + } } return 0; @@ -319,6 +341,7 @@ int SortSeqsCommand::readFasta(){ int times = 0; vector seqs; seqs.resize(size); + for (int i = 0; i < seqs.size(); i++) { seqs[i].setName(""); } //this is so if some of the seqs are missing we dont print out garbage while (numLeft > 0) { @@ -363,7 +386,7 @@ int SortSeqsCommand::readFasta(){ if (numLeft < seqs.size()) { output = numLeft; } for (int i = 0; i < output; i++) { - seqs[i].printSequence(out2); + if (seqs[i].getName() != "") { seqs[i].printSequence(out2); } } out2.close(); @@ -375,6 +398,7 @@ int SortSeqsCommand::readFasta(){ }else { vector seqs; seqs.resize(names.size()); + for (int i = 0; i < seqs.size(); i++) { seqs[i].setName(""); } //this is so if some of the seqs are missing we dont print out garbage while(!in.eof()){ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } @@ -396,12 +420,15 @@ int SortSeqsCommand::readFasta(){ } in.close(); + int count = 0; for (int i = 0; i < seqs.size(); i++) { - seqs[i].printSequence(out); + if (seqs[i].getName() != "") { + seqs[i].printSequence(out); count++; + } } out.close(); - m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + fastafile + ".\n"); + m->mothurOut("Ordered " + toString(count) + " sequences from " + fastafile + ".\n"); } }else { //read in file to fill names @@ -435,6 +462,184 @@ int SortSeqsCommand::readFasta(){ exit(1); } } +//********************************************************************************************************************** +int SortSeqsCommand::readFlow(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(flowfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(flowfile)) + "sorted" + m->getExtension(flowfile); + outputTypes["flow"].push_back(outputFileName); outputNames.push_back(outputFileName); + + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(flowfile, in); + int numFlows; + string name; + + in >> numFlows; m->gobble(in); + + if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have + + if (large) { //if the file is too large to fit in memory we can still process it, but the io will be very time consuming. + //read through the file looking for 1000 seqs at a time. Once we find them output them and start looking for the next 1000. + //this way we only store 1000 seqs in memory at a time. + + int numNames = names.size(); + int numNamesInFile = 0; + + //to make sure we dont miss any seqs, add any seqs that are not in names but in the file to the end of names + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> name; + string rest = m->getline(in); + + if (name != "") { + numNamesInFile++; + map::iterator it = names.find(name); + if (it == names.end()) { + names[name] = numNames; numNames++; + m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n"); + } + } + m->gobble(in); + } + in.close(); + out.close(); + + int numLeft = names.size(); + if (numNamesInFile < numLeft) { numLeft = numNamesInFile; } + + int size = 1000; //assume that user can hold 1000 seqs in memory + if (numLeft < size) { size = numLeft; } + int times = 0; + + vector seqs; seqs.resize(size, ""); + + while (numLeft > 0) { + + ifstream in2; + m->openInputFile(flowfile, in2); in2 >> numFlows; m->gobble(in2); + + if (m->control_pressed) { in2.close(); m->mothurRemove(outputFileName); return 0; } + + int found = 0; + int needToFind = size; + if (numLeft < size) { needToFind = numLeft; } + + while(!in2.eof()){ + if (m->control_pressed) { in2.close(); m->mothurRemove(outputFileName); return 0; } + + //stop reading if we already found the seqs we are looking for + if (found >= needToFind) { break; } + + in2 >> name; + string rest = m->getline(in2); + + if (name != "") { + map::iterator it = names.find(name); + if (it != names.end()) { //we found it, so put it in the vector in the right place. + //is it in the set of seqs we are looking for this time around + int thisSeqsPlace = it->second; + thisSeqsPlace -= (times * size); + if ((thisSeqsPlace < size) && (thisSeqsPlace >= 0)) { + seqs[thisSeqsPlace] = (name +'\t' + rest); + found++; + } + }else { m->mothurOut("[ERROR]: in logic of readFlow function.\n"); m->control_pressed = true; } + } + m->gobble(in2); + } + in2.close(); + + ofstream out2; + m->openOutputFileAppend(outputFileName, out2); + + int output = seqs.size(); + if (numLeft < seqs.size()) { output = numLeft; } + + for (int i = 0; i < output; i++) { + if (seqs[i] != "") { + out2 << seqs[i] << endl; + } + } + out2.close(); + + times++; + numLeft -= output; + } + + m->mothurOut("Ordered " + toString(numNamesInFile) + " flows from " + flowfile + ".\n"); + }else { + + vector seqs; seqs.resize(names.size(), ""); + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> name; + string rest = m->getline(in); + + if (name != "") { + map::iterator it = names.find(name); + if (it != names.end()) { //we found it, so put it in the vector in the right place. + seqs[it->second] = (name + '\t' + rest); + }else { //if we cant find it then add it to the end + names[name] = seqs.size(); + seqs.push_back((name + '\t' + rest)); + m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n"); + } + } + m->gobble(in); + } + in.close(); + + int count = 0; + for (int i = 0; i < seqs.size(); i++) { + if (seqs[i] != "") { + out << seqs[i] << endl; + count++; + } + } + out.close(); + + m->mothurOut("Ordered " + toString(count) + " flows from " + flowfile + ".\n"); + } + + }else { //read in file to fill names + int count = 0; + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> name; + string rest = m->getline(in); + + if (name != "") { + //if this name is in the accnos file + names[name] = count; + count++; + out << name << '\t' << rest << endl; + } + m->gobble(in); + } + in.close(); + out.close(); + + m->mothurOut("\nUsing " + flowfile + " to determine the order. It contains " + toString(count) + " flows.\n"); + } + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "readFlow"); + exit(1); + } +} + //********************************************************************************************************************** int SortSeqsCommand::readQual(){ try { @@ -489,6 +694,7 @@ int SortSeqsCommand::readQual(){ vector seqs; seqs.resize(size); + for (int i = 0; i < seqs.size(); i++) { seqs[i].setName(""); } //this is so if some of the seqs are missing we dont print out garbage while (numLeft > 0) { @@ -534,7 +740,9 @@ int SortSeqsCommand::readQual(){ if (numLeft < seqs.size()) { output = numLeft; } for (int i = 0; i < output; i++) { - seqs[i].printQScores(out2); + if (seqs[i].getName() != "") { + seqs[i].printQScores(out2); + } } out2.close(); @@ -547,6 +755,7 @@ int SortSeqsCommand::readQual(){ }else { vector seqs; seqs.resize(names.size()); + for (int i = 0; i < seqs.size(); i++) { seqs[i].setName(""); } //this is so if some of the seqs are missing we dont print out garbage while(!in.eof()){ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } @@ -569,12 +778,13 @@ int SortSeqsCommand::readQual(){ } in.close(); + int count = 0; for (int i = 0; i < seqs.size(); i++) { - seqs[i].printQScores(out); + if (seqs[i].getName() != "") { seqs[i].printQScores(out); count++; } } out.close(); - m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + qualfile + ".\n"); + m->mothurOut("Ordered " + toString(count) + " sequences from " + qualfile + ".\n"); } }else { //read in file to fill names @@ -627,7 +837,7 @@ int SortSeqsCommand::readName(){ if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have - vector seqs; seqs.resize(names.size()); + vector seqs; seqs.resize(names.size(), ""); while(!in.eof()){ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } @@ -648,12 +858,13 @@ int SortSeqsCommand::readName(){ } in.close(); + int count = 0; for (int i = 0; i < seqs.size(); i++) { - out << seqs[i] << endl; + if (seqs[i] != "") { out << seqs[i] << endl; count++; } } out.close(); - m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + namefile + ".\n"); + m->mothurOut("Ordered " + toString(count) + " sequences from " + namefile + ".\n"); }else { //read in file to fill names int count = 0; @@ -703,7 +914,7 @@ int SortSeqsCommand::readGroup(){ if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have - vector seqs; seqs.resize(names.size()); + vector seqs; seqs.resize(names.size(), ""); while(!in.eof()){ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } @@ -724,12 +935,13 @@ int SortSeqsCommand::readGroup(){ } in.close(); + int count = 0; for (int i = 0; i < seqs.size(); i++) { - out << seqs[i] << endl; + if (seqs[i] != "") { out << seqs[i] << endl; count++; } } out.close(); - m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + groupfile + ".\n"); + m->mothurOut("Ordered " + toString(count) + " sequences from " + groupfile + ".\n"); }else { //read in file to fill names int count = 0; @@ -778,7 +990,7 @@ int SortSeqsCommand::readTax(){ if (names.size() != 0) {//this is not the first file we are reading so we need to use the order we already have - vector seqs; seqs.resize(names.size()); + vector seqs; seqs.resize(names.size(), ""); while(!in.eof()){ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } @@ -799,12 +1011,13 @@ int SortSeqsCommand::readTax(){ } in.close(); + int count = 0; for (int i = 0; i < seqs.size(); i++) { - out << seqs[i] << endl; + if (seqs[i] != "") { out << seqs[i] << endl; count++; } } out.close(); - m->mothurOut("Ordered " + toString(seqs.size()) + " sequences from " + taxfile + ".\n"); + m->mothurOut("Ordered " + toString(count) + " sequences from " + taxfile + ".\n"); }else { //read in file to fill names int count = 0;