X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sortseqscommand.cpp;fp=sortseqscommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=0236a505d7dafb683ebe188bbad768a88ca5a5c3;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/sortseqscommand.cpp b/sortseqscommand.cpp deleted file mode 100644 index 0236a50..0000000 --- a/sortseqscommand.cpp +++ /dev/null @@ -1,1090 +0,0 @@ -// -// 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); - } -} - -//********************************************************************************************************************** - - - - -