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getseqscommand.cpp
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getseqscommand.cpp
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/*
* getseqscommand.cpp
* Mothur
*
* Created by Sarah Westcott on 7/8/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "getseqscommand.h"
#include "sequence.hpp"
#include "listvector.hpp"
#include "counttable.h"
//**********************************************************************************************************************
vector<string> GetSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false,true); parameters.push_back(pgroup);
CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none","qfile",false,false); parameters.push_back(pqfile);
CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
CommandParameter pdups("dups", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pdups);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos2);
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, "GetSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string GetSeqsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, count, list, taxonomy, quality or alignreport file.\n";
helpString += "It outputs a file containing only the sequences in the .accnos file.\n";
helpString += "The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups. You must provide accnos unless you have a valid current accnos file, and at least one of the other parameters.\n";
helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=true. \n";
helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n";
helpString += "Example get.seqs(accnos=amazon.accnos, 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, "GetSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
GetSeqsCommand::GetSeqsCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["alignreport"] = tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["count"] = tempOutNames;
outputTypes["accnosreport"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
exit(1);
}
}
//**********************************************************************************************************************
string GetSeqsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],pick,[extension]"; }
else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; }
else if (type == "name") { pattern = "[filename],pick,[extension]"; }
else if (type == "group") { pattern = "[filename],pick,[extension]"; }
else if (type == "count") { pattern = "[filename],pick,[extension]"; }
else if (type == "list") { pattern = "[filename],pick,[extension]"; }
else if (type == "qfile") { pattern = "[filename],pick,[extension]"; }
else if (type == "accnosreport") { pattern = "[filename],pick.accnos.report"; }
else if (type == "alignreport") { pattern = "[filename],pick.align.report"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
GetSeqsCommand::GetSeqsCommand(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["alignreport"] = tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["qfile"] = tempOutNames;
outputTypes["accnosreport"] = tempOutNames;
outputTypes["count"] = 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("alignreport");
//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["alignreport"] = inputDir + it->second; }
}
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("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("accnos2");
//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["accnos2"] = inputDir + it->second; }
}
it = parameters.find("list");
//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["list"] = 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("count");
//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["count"] = inputDir + it->second; }
}
}
//check for required parameters
accnosfile = validParameter.validFile(parameters, "accnos", true);
if (accnosfile == "not open") { abort = true; }
else if (accnosfile == "not found") {
accnosfile = m->getAccnosFile();
if (accnosfile != "") { m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
abort = true;
}
}else { m->setAccnosFile(accnosfile); }
if (accnosfile2 == "not found") { accnosfile2 = ""; }
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { fastafile = ""; abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
else { m->setFastaFile(fastafile); }
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); }
alignfile = validParameter.validFile(parameters, "alignreport", true);
if (alignfile == "not open") { abort = true; }
else if (alignfile == "not found") { alignfile = ""; }
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
else if (listfile == "not found") { listfile = ""; }
else { m->setListFile(listfile); }
taxfile = validParameter.validFile(parameters, "taxonomy", true);
if (taxfile == "not open") { taxfile = ""; 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); }
accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
if (accnosfile2 == "not open") { abort = true; }
else if (accnosfile2 == "not found") { accnosfile2 = ""; }
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else { m->setCountTableFile(countfile); }
if ((namefile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
}
if ((groupfile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
}
string usedDups = "true";
string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "true"; usedDups = ""; }
dups = m->isTrue(temp);
if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "") && (accnosfile2 == "") && (countfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, count, alignreport, taxonomy, quality or listfile."); m->mothurOutEndLine(); abort = true; }
if (countfile == "") {
if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
parser.getNameFile(files);
}
}
}
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
exit(1);
}
}
//**********************************************************************************************************************
int GetSeqsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get names you want to keep
names = m->readAccnos(accnosfile);
if (m->control_pressed) { return 0; }
if (countfile != "") {
if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
}
}
//read through the correct file and output lines you want to keep
if (namefile != "") { readName(); }
if (fastafile != "") { readFasta(); }
if (groupfile != "") { readGroup(); }
if (countfile != "") { readCount(); }
if (alignfile != "") { readAlign(); }
if (listfile != "") { readList(); }
if (taxfile != "") { readTax(); }
if (qualfile != "") { readQual(); }
if (accnosfile2 != "") { compareAccnos(); }
if (m->debug) { runSanityCheck(); }
if (m->control_pressed) { outputTypes.clear(); 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("list");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(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("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int GetSeqsCommand::readFasta(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
variables["[extension]"] = m->getExtension(fastafile);
string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(fastafile, in);
string name;
bool wroteSomething = false;
int selectedCount = 0;
if (m->debug) { set<string> temp; sanity["fasta"] = temp; }
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
Sequence currSeq(in);
name = currSeq.getName();
if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(name);
if (it != uniqueMap.end()) { currSeq.setName(it->second); }
}
name = currSeq.getName();
if (name != "") {
//if this name is in the accnos file
if (names.count(name) != 0) {
wroteSomething = true;
currSeq.printSequence(out);
selectedCount++;
if (m->debug) { sanity["fasta"].insert(name); }
}
}
m->gobble(in);
}
in.close();
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "readFasta");
exit(1);
}
}
//**********************************************************************************************************************
int GetSeqsCommand::readQual(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(qualfile));
variables["[extension]"] = m->getExtension(qualfile);
string outputFileName = getOutputFileName("qfile", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(qualfile, in);
string name;
bool wroteSomething = false;
int selectedCount = 0;
if (m->debug) { set<string> temp; sanity["qual"] = temp; }
while(!in.eof()){
string saveName = "";
string name = "";
string scores = "";
in >> name;
if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(name);
if (it != uniqueMap.end()) { name = it->second; }
}
if (name.length() != 0) {
saveName = name.substr(1);
while (!in.eof()) {
char c = in.get();
if (c == 10 || c == 13 || c == -1){ break; }
else { name += c; }
}
m->gobble(in);
}
while(in){
char letter= in.get();
if(letter == '>'){ in.putback(letter); break; }
else{ scores += letter; }
}
m->gobble(in);
if (names.count(saveName) != 0) {
wroteSomething = true;
out << name << endl << scores;
selectedCount++;
if (m->debug) { sanity["qual"].insert(name); }
}
m->gobble(in);
}
in.close();
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["qfile"].push_back(outputFileName);
m->mothurOut("Selected " + toString(selectedCount) + " sequences from your quality file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "readQual");
exit(1);
}
}
//**********************************************************************************************************************
int GetSeqsCommand::readCount(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
variables["[extension]"] = m->getExtension(countfile);
string outputFileName = getOutputFileName("count", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(countfile, in);
bool wroteSomething = false;
int selectedCount = 0;
string headers = m->getline(in); m->gobble(in);
out << headers << endl;
string name, rest; int thisTotal;
while (!in.eof()) {
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> name; m->gobble(in);
in >> thisTotal; m->gobble(in);
rest = m->getline(in); m->gobble(in);
if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); }
if (names.count(name) != 0) {
out << name << '\t' << thisTotal << '\t' << rest << endl;
wroteSomething = true;
selectedCount+= thisTotal;
}
}
in.close();
out.close();
//check for groups that have been eliminated
CountTable ct;
if (ct.testGroups(outputFileName)) {
ct.readTable(outputFileName, true);
ct.printTable(outputFileName);
}
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->mothurOut("Selected " + toString(selectedCount) + " sequences from your count file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "readCount");
exit(1);
}
}
//**********************************************************************************************************************
int GetSeqsCommand::readList(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
variables["[extension]"] = m->getExtension(listfile);
string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(listfile, in);
bool wroteSomething = false;
int selectedCount = 0;
if (m->debug) { set<string> temp; sanity["list"] = temp; }
while(!in.eof()){
selectedCount = 0;
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
//read in list vector
ListVector list(in);
//make a new list vector
ListVector newList;
newList.setLabel(list.getLabel());
//for each bin
for (int i = 0; i < list.getNumBins(); i++) {
//parse out names that are in accnos file
string binnames = list.get(i);
vector<string> bnames;
m->splitAtComma(binnames, bnames);
string newNames = "";
for (int i = 0; i < bnames.size(); i++) {
string name = bnames[i];
//if that name is in the .accnos file, add it
if (names.count(name) != 0) { newNames += name + ","; selectedCount++; if (m->debug) { sanity["list"].insert(name); } }
}
//if there are names in this bin add to new list
if (newNames != "") {
newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
newList.push_back(newNames);
}
}
//print new listvector
if (newList.getNumBins() != 0) {
wroteSomething = true;
newList.print(out);
}
m->gobble(in);
}
in.close();
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "readList");
exit(1);
}
}
//**********************************************************************************************************************
int GetSeqsCommand::readName(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
variables["[extension]"] = m->getExtension(namefile);
string outputFileName = getOutputFileName("name", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(namefile, in);
string name, firstCol, secondCol;
bool wroteSomething = false;
int selectedCount = 0;
if (m->debug) { set<string> temp; sanity["name"] = temp; }
if (m->debug) { set<string> temp; sanity["dupname"] = temp; }
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> firstCol; m->gobble(in);
in >> secondCol;
string hold = "";
if (dups) { hold = secondCol; }
vector<string> parsedNames;
m->splitAtComma(secondCol, parsedNames);
vector<string> validSecond;
for (int i = 0; i < parsedNames.size(); i++) {
if (names.count(parsedNames[i]) != 0) {
validSecond.push_back(parsedNames[i]);
if (m->debug) { sanity["dupname"].insert(parsedNames[i]); }
}
}
if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); if (m->debug) { sanity["dupname"].insert(parsedNames[i]); } }
out << firstCol << '\t' << hold << endl;
wroteSomething = true;
selectedCount += parsedNames.size();
if (m->debug) { sanity["name"].insert(firstCol); }
}else {
selectedCount += validSecond.size();
//if the name in the first column is in the set then print it and any other names in second column also in set
if (names.count(firstCol) != 0) {
wroteSomething = true;
out << firstCol << '\t';
//you know you have at least one valid second since first column is valid
for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
out << validSecond[validSecond.size()-1] << endl;
if (m->debug) { sanity["name"].insert(firstCol); }
//make first name in set you come to first column and then add the remaining names to second column
}else {
//you want part of this row
if (validSecond.size() != 0) {
wroteSomething = true;
out << validSecond[0] << '\t';
//we are changing the unique name in the fasta file
uniqueMap[firstCol] = validSecond[0];
//you know you have at least one valid second since first column is valid
for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
out << validSecond[validSecond.size()-1] << endl;
if (m->debug) { sanity["name"].insert(validSecond[0]); }
}
}
}
m->gobble(in);
}
in.close();
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "readName");
exit(1);
}
}
//**********************************************************************************************************************
int GetSeqsCommand::readGroup(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
variables["[extension]"] = m->getExtension(groupfile);
string outputFileName = getOutputFileName("group", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(groupfile, in);
string name, group;
bool wroteSomething = false;
int selectedCount = 0;
if (m->debug) { set<string> temp; sanity["group"] = temp; }
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> name; //read from first column
in >> group; //read from second column
//if this name is in the accnos file
if (names.count(name) != 0) {
wroteSomething = true;
out << name << '\t' << group << endl;
selectedCount++;
if (m->debug) { sanity["group"].insert(name); }
}
m->gobble(in);
}
in.close();
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "readGroup");
exit(1);
}
}
//**********************************************************************************************************************
int GetSeqsCommand::readTax(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
variables["[extension]"] = m->getExtension(taxfile);
string outputFileName = getOutputFileName("taxonomy", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(taxfile, in);
string name, tax;
bool wroteSomething = false;
int selectedCount = 0;
if (m->debug) { set<string> temp; sanity["tax"] = temp; }
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> name; //read from first column
in >> tax; //read from second column
if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(name);
if (it != uniqueMap.end()) { name = it->second; }
}
//if this name is in the accnos file
if (names.count(name) != 0) {
wroteSomething = true;
out << name << '\t' << tax << endl;
selectedCount++;
if (m->debug) { sanity["tax"].insert(name); }
}
m->gobble(in);
}
in.close();
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
m->mothurOut("Selected " + toString(selectedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "readTax");
exit(1);
}
}
//**********************************************************************************************************************
//alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name
int GetSeqsCommand::readAlign(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(alignfile));
string outputFileName = getOutputFileName("alignreport", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(alignfile, in);
string name, junk;
bool wroteSomething = false;
int selectedCount = 0;
//read column headers
for (int i = 0; i < 16; i++) {
if (!in.eof()) { in >> junk; out << junk << '\t'; }
else { break; }
}
out << endl;
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> name; //read from first column
if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(name);
if (it != uniqueMap.end()) { name = it->second; }
}
//if this name is in the accnos file
if (names.count(name) != 0) {
wroteSomething = true;
selectedCount++;
out << name << '\t';
//read rest
for (int i = 0; i < 15; i++) {
if (!in.eof()) { in >> junk; out << junk << '\t'; }
else { break; }
}
out << endl;
}else {//still read just don't do anything with it
//read rest
for (int i = 0; i < 15; i++) {
if (!in.eof()) { in >> junk; }
else { break; }
}
}
m->gobble(in);
}
in.close();
out.close();
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
m->mothurOut("Selected " + toString(selectedCount) + " sequences from your alignreport file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "readAlign");
exit(1);
}
}
//**********************************************************************************************************************
//just looking at common mistakes.
int GetSeqsCommand::runSanityCheck(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }