X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sortseqscommand.cpp;fp=sortseqscommand.cpp;h=0236a505d7dafb683ebe188bbad768a88ca5a5c3;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git diff --git a/sortseqscommand.cpp b/sortseqscommand.cpp new file mode 100644 index 0000000..0236a50 --- /dev/null +++ b/sortseqscommand.cpp @@ -0,0 +1,1090 @@ +// +// sortseqscommand.cpp +// Mothur +// +// Created by Sarah Westcott on 2/3/12. +// Copyright (c) 2012 Schloss Lab. All rights reserved. +// + +#include "sortseqscommand.h" +#include "sequence.hpp" +#include "qualityscores.h" + +//********************************************************************************************************************** +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); + CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile); + CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge); + CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos); + 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, "SortSeqsCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +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, 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"; + helpString += "Example sort.seqs(fasta=amazon.fasta).\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, "SortSeqsCommand", "getHelpString"); + exit(1); + } +} + + +//********************************************************************************************************************** +SortSeqsCommand::SortSeqsCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["taxonomy"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["qfile"] = tempOutNames; + outputTypes["flow"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "SortSeqsCommand"); + exit(1); + } +} +//********************************************************************************************************************** +SortSeqsCommand::SortSeqsCommand(string option) { + try { + abort = false; calledHelp = false; + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} + + else { + vector myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + map::iterator it; + + //check to make sure all parameters are valid for command + for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["taxonomy"] = tempOutNames; + 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 = ""; } + + //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 = ""; } + else { + string path; + it = parameters.find("fasta"); + //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["fasta"] = inputDir + it->second; } + } + + it = parameters.find("name"); + //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["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; } + } + + it = parameters.find("taxonomy"); + //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["taxonomy"] = inputDir + it->second; } + } + + it = parameters.find("qfile"); + //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["qfile"] = inputDir + it->second; } + } + + it = parameters.find("accnos"); + //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["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; } + } + } + + + //check for parameters + accnosfile = validParameter.validFile(parameters, "accnos", true); + if (accnosfile == "not open") { accnosfile = ""; abort = true; } + else if (accnosfile == "not found") { accnosfile = ""; } + else { m->setAccnosFile(accnosfile); } + + fastafile = validParameter.validFile(parameters, "fasta", true); + if (fastafile == "not open") { fastafile = ""; abort = true; } + 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 = ""; } + else { m->setNameFile(namefile); } + + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not open") { abort = true; } + else if (groupfile == "not found") { groupfile = ""; } + else { m->setGroupFile(groupfile); } + + taxfile = validParameter.validFile(parameters, "taxonomy", true); + if (taxfile == "not open") { abort = true; } + else if (taxfile == "not found") { taxfile = ""; } + else { m->setTaxonomyFile(taxfile); } + + qualfile = validParameter.validFile(parameters, "qfile", true); + if (qualfile == "not open") { abort = true; } + else if (qualfile == "not found") { qualfile = ""; } + else { m->setQualFile(qualfile); } + + string temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "f"; } + large = m->isTrue(temp); + + 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); + parser.getNameFile(files); + } + } + + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "SortSeqsCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +int SortSeqsCommand::execute(){ + try { + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + //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(); } + if (taxfile != "") { readTax(); } + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + if (outputNames.size() != 0) { + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + 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); } + } + + itTypes = outputTypes.find("group"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); } + } + + + itTypes = outputTypes.find("taxonomy"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); } + } + + 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; + } + + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "execute"); + exit(1); + } +} + +//********************************************************************************************************************** +int SortSeqsCommand::readFasta(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "sorted" + m->getExtension(fastafile); + outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName); + + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(fastafile, in); + string name; + + 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; } + + Sequence currSeq(in); + name = currSeq.getName(); + + 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); + 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) { + + ifstream in2; + m->openInputFile(fastafile, 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; } + + Sequence currSeq(in2); + name = currSeq.getName(); + + 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] = currSeq; + found++; + } + }else { m->mothurOut("[ERROR]: in logic of readFasta 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].getName() != "") { seqs[i].printSequence(out2); } + } + out2.close(); + + times++; + numLeft -= output; + } + + m->mothurOut("Ordered " + toString(numNamesInFile) + " sequences from " + fastafile + ".\n"); + }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; } + + Sequence currSeq(in); + name = currSeq.getName(); + + 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] = currSeq; + }else { //if we cant find it then add it to the end + names[name] = seqs.size(); + seqs.push_back(currSeq); + 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].getName() != "") { + seqs[i].printSequence(out); count++; + } + } + out.close(); + + m->mothurOut("Ordered " + toString(count) + " sequences from " + fastafile + ".\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; } + + Sequence currSeq(in); + name = currSeq.getName(); + + if (name != "") { + //if this name is in the accnos file + names[name] = count; + count++; + currSeq.printSequence(out); + } + m->gobble(in); + } + in.close(); + out.close(); + + m->mothurOut("\nUsing " + fastafile + " to determine the order. It contains " + toString(count) + " sequences.\n"); + } + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "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 { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "sorted" + m->getExtension(qualfile); + outputTypes["qfile"].push_back(outputFileName); outputNames.push_back(outputFileName); + + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(qualfile, in); + string name; + + 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; } + + QualityScores currQual; + currQual = QualityScores(in); + name = currQual.getName(); + + 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); + 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) { + + ifstream in2; + m->openInputFile(qualfile, 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; } + + QualityScores currQual; + currQual = QualityScores(in2); + name = currQual.getName(); + + 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] = currQual; + found++; + } + }else { m->mothurOut("[ERROR]: in logic of readQual 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].getName() != "") { + seqs[i].printQScores(out2); + } + } + out2.close(); + + times++; + numLeft -= output; + } + + m->mothurOut("Ordered " + toString(numNamesInFile) + " sequences from " + qualfile + ".\n"); + + }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; } + + QualityScores currQual; + currQual = QualityScores(in); + name = currQual.getName(); + + 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] = currQual; + }else { //if we cant find it then add it to the end + names[name] = seqs.size(); + seqs.push_back(currQual); + 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].getName() != "") { seqs[i].printQScores(out); count++; } + } + out.close(); + + m->mothurOut("Ordered " + toString(count) + " sequences from " + qualfile + ".\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; } + + QualityScores currQual; + currQual = QualityScores(in); + + m->gobble(in); + + if (currQual.getName() != "") { + //if this name is in the accnos file + names[currQual.getName()] = count; + count++; + currQual.printQScores(out); + } + m->gobble(in); + } + in.close(); + out.close(); + + m->mothurOut("\nUsing " + qualfile + " to determine the order. It contains " + toString(count) + " sequences.\n"); + } + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "readQual"); + exit(1); + } +} +//********************************************************************************************************************** +int SortSeqsCommand::readName(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(namefile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "sorted" + m->getExtension(namefile); + outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName); + + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(namefile, in); + string name, firstCol, secondCol; + + 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(), ""); + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> firstCol; m->gobble(in); + in >> secondCol; m->gobble(in); + + if (firstCol != "") { + map::iterator it = names.find(firstCol); + if (it != names.end()) { //we found it, so put it in the vector in the right place. + seqs[it->second] = firstCol + '\t' + secondCol; + }else { //if we cant find it then add it to the end + names[firstCol] = seqs.size(); + seqs.push_back((firstCol + '\t' + secondCol)); + m->mothurOut(firstCol + " was not in the contained the file which determined the order, adding it to the end.\n"); + } + } + } + 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) + " sequences from " + namefile + ".\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 >> firstCol; m->gobble(in); + in >> secondCol; m->gobble(in); + + if (firstCol != "") { + //if this name is in the accnos file + names[firstCol] = count; + count++; + out << firstCol << '\t' << secondCol << endl; + } + m->gobble(in); + } + in.close(); + out.close(); + + m->mothurOut("\nUsing " + namefile + " to determine the order. It contains " + toString(count) + " representative sequences.\n"); + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "readName"); + exit(1); + } +} + +//********************************************************************************************************************** +int SortSeqsCommand::readGroup(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile); + outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName); + + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(groupfile, in); + string name, group; + + 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(), ""); + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> name; m->gobble(in); + in >> group; m->gobble(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' + group; + }else { //if we cant find it then add it to the end + names[name] = seqs.size(); + seqs.push_back((name + '\t' + group)); + m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n"); + } + } + } + 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) + " sequences from " + groupfile + ".\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; m->gobble(in); + in >> group; m->gobble(in); + + if (name != "") { + //if this name is in the accnos file + names[name] = count; + count++; + out << name << '\t' << group << endl; + } + m->gobble(in); + } + in.close(); + out.close(); + + m->mothurOut("\nUsing " + groupfile + " to determine the order. It contains " + toString(count) + " sequences.\n"); + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "readGroup"); + exit(1); + } +} +//********************************************************************************************************************** +int SortSeqsCommand::readTax(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile); + outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName); + + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(taxfile, in); + string name, tax; + + 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(), ""); + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> name; m->gobble(in); + in >> tax; m->gobble(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' + tax; + }else { //if we cant find it then add it to the end + names[name] = seqs.size(); + seqs.push_back((name + '\t' + tax)); + m->mothurOut(name + " was not in the contained the file which determined the order, adding it to the end.\n"); + } + } + } + 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) + " sequences from " + taxfile + ".\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; m->gobble(in); + in >> tax; m->gobble(in); + + if (name != "") { + //if this name is in the accnos file + names[name] = count; + count++; + out << name << '\t' << tax << endl; + } + m->gobble(in); + } + in.close(); + out.close(); + + m->mothurOut("\nUsing " + taxfile + " to determine the order. It contains " + toString(count) + " sequences.\n"); + } + + return 0; + return 0; + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "readTax"); + exit(1); + } +} +//********************************************************************************************************************** +int SortSeqsCommand::readAccnos(){ + try { + + ifstream in; + m->openInputFile(accnosfile, in); + string name; + int count = 0; + + while(!in.eof()){ + + if (m->control_pressed) { break; } + + in >> name; m->gobble(in); + + if (name != "") { + names[name] = count; + count++; + } + } + in.close(); + + m->mothurOut("\nUsing " + accnosfile + " to determine the order. It contains " + toString(count) + " representative sequences.\n"); + + return 0; + } + catch(exception& e) { + m->errorOut(e, "SortSeqsCommand", "readAccnos"); + exit(1); + } +} + +//********************************************************************************************************************** + + + + +