+++ /dev/null
-//
-// 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<string> 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<string> 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<string> 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<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
-
- ValidParameters validParameter;
- map<string,string>::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<string> 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<string> 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<string, int>::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<Sequence> 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<string, int>::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<Sequence> 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<string, int>::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<string, int>::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<string> 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<string, int>::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<string> 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<string, int>::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<string, int>::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<QualityScores> 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<string, int>::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<QualityScores> 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<string, int>::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<string> 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<string, int>::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<string> 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<string, int>::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<string> 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<string, int>::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);
- }
-}
-
-//**********************************************************************************************************************
-
-
-
-
-
projects / mothur.git / blobdiff