#include "splitabundcommand.h"
+//**********************************************************************************************************************
+vector<string> SplitAbundCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "",false,true); parameters.push_back(pcutoff);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter paccnos("accnos", "Boolean", "", "F", "", "", "",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, "SplitAbundCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SplitAbundCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The split.abund command reads a fasta file and a list or a names file splits the sequences into rare and abundant groups. \n";
+ helpString += "The split.abund command parameters are fasta, list, name, cutoff, group, label, groups, cutoff and accnos.\n";
+ helpString += "The fasta and a list or name parameter are required, and you must provide a cutoff value.\n";
+ helpString += "The cutoff parameter is used to qualify what is abundant and rare.\n";
+ helpString += "The group parameter allows you to parse a group file into rare and abundant groups.\n";
+ helpString += "The label parameter is used to read specific labels in your listfile you want to use.\n";
+ helpString += "The accnos parameter allows you to output a .rare.accnos and .abund.accnos files to use with the get.seqs and remove.seqs commands.\n";
+ helpString += "The groups parameter allows you to parse the files into rare and abundant files by group. \n";
+ helpString += "For example if you set groups=A-B-C, you will get a .A.abund, .A.rare, .B.abund, .B.rare, .C.abund, .C.rare files. \n";
+ helpString += "If you want .abund and .rare files for all groups, set groups=all. \n";
+ helpString += "The split.abund command should be used in the following format: split.abund(fasta=yourFasta, list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n";
+ helpString += "Example: split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, cutoff=2).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SplitAbundCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "fasta") { outputFileName = "fasta"; }
+ else if (type == "list") { outputFileName = "list"; }
+ else if (type == "name") { outputFileName = "names"; }
+ else if (type == "group") { outputFileName = "groups"; }
+ else if (type == "accnos") { outputFileName = "accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SplitAbundCommand::SplitAbundCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "SplitAbundCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
SplitAbundCommand::SplitAbundCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
- if(option == "help") { help(); abort = true; }
-
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"name","group","list","label","accnos","groups","fasta","cutoff","outputdir","inputdir"}; //
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
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["list"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+
//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 = ""; }
it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ 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("group");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ 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("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ 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 = hasPath(it->second);
+ 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; }
}
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
else if (listfile == "not found") { listfile = ""; }
- else{ inputFile = listfile; }
+ else{ inputFile = listfile; m->setListFile(listfile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
- else{ inputFile = namefile; }
+ else{ inputFile = namefile; m->setNameFile(namefile); }
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the split.abund command. "); m->mothurOutEndLine(); abort = true; }
+ else if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setFastaFile(fastafile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { groupfile = ""; abort = true; }
int error = groupMap->readMap();
if (error == 1) { abort = true; }
-
+ m->setGroupFile(groupfile);
}
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else if (groups == "all") {
- if (groupfile != "") { Groups = groupMap->namesOfGroups; }
+ if (groupfile != "") { Groups = groupMap->getNamesOfGroups(); }
else { m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = ""; }
}else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
}
if ((groupfile == "") && (groups != "")) { m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = ""; Groups.clear(); }
//do you have all files needed
- if ((listfile == "") && (namefile == "")) { m->mothurOut("You must either a listfile or a namefile for the split.abund command. "); m->mothurOutEndLine(); abort = true; }
+ if ((listfile == "") && (namefile == "")) {
+ namefile = m->getNameFile();
+ if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
+ else {
+ listfile = m->getListFile();
+ if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current list or namefile and the list or name parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+ }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; allLines = 1; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
string temp = validParameter.validFile(parameters, "accnos", false); if (temp == "not found") { temp = "F"; }
- accnos = isTrue(temp);
+ accnos = m->isTrue(temp);
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "0"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
if (cutoff == 0) { m->mothurOut("You must provide a cutoff to qualify what is abundant for the split.abund command. "); m->mothurOutEndLine(); abort = true; }
-
}
}
}
}
//**********************************************************************************************************************
-void SplitAbundCommand::help(){
- try {
- m->mothurOut("The split.abund command reads a fasta file and a list or a names file splits the sequences into rare and abundant groups. \n");
- m->mothurOut("The split.abund command parameters are fasta, list, name, cutoff, group, label, groups, cutoff and accnos.\n");
- m->mothurOut("The fasta and a list or name parameter are required, and you must provide a cutoff value.\n");
- m->mothurOut("The cutoff parameter is used to qualify what is abundant and rare.\n");
- m->mothurOut("The group parameter allows you to parse a group file into rare and abundant groups.\n");
- m->mothurOut("The label parameter is used to read specific labels in your listfile you want to use.\n");
- m->mothurOut("The accnos parameter allows you to output a .rare.accnos and .abund.accnos files to use with the get.seqs and remove.seqs commands.\n");
- m->mothurOut("The groups parameter allows you to parse the files into rare and abundant files by group. \n");
- m->mothurOut("For example if you set groups=A-B-C, you will get a .A.abund, .A.rare, .B.abund, .B.rare, .C.abund, .C.rare files. \n");
- m->mothurOut("If you want .abund and .rare files for all groups, set groups=all. \n");
- m->mothurOut("The split.abund command should be used in the following format: split.abund(fasta=yourFasta, list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n");
- m->mothurOut("Example: split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, cutoff=2).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "SplitAbundCommand", "help");
- exit(1);
- }
-}
-//**********************************************************************************************************************
SplitAbundCommand::~SplitAbundCommand(){
if (groupfile != "") { delete groupMap; }
}
int SplitAbundCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (listfile != "") { //you are using a listfile to determine abundance
- if (outputDir == "") { outputDir = hasPath(listfile); }
-
- //remove old files so you can append later....
- string fileroot = outputDir + getRootName(getSimpleName(listfile));
- if (Groups.size() == 0) {
- remove((fileroot + "rare.list").c_str());
- remove((fileroot + "abund.list").c_str());
-
- wroteListFile["rare"] = false;
- wroteListFile["abund"] = false;
- }else{
- for (int i=0; i<Groups.size(); i++) {
- remove((fileroot + Groups[i] + ".rare.list").c_str());
- remove((fileroot + Groups[i] + ".abund.list").c_str());
-
- wroteListFile[(Groups[i] + ".rare")] = false;
- wroteListFile[(Groups[i] + ".abund")] = false;
- }
- }
+ if (outputDir == "") { outputDir = m->hasPath(listfile); }
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
if (namefile != "") { readNamesFile(); }
else { createNameMap(list); }
- if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if(allLines == 1 || labels.count(list->getLabel()) == 1){
userLabels.erase(list->getLabel());
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
delete list;
list = input->getListVector(); //get new list vector to process
}
- if (m->control_pressed) { delete input; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
- if (m->control_pressed) { delete input; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//run last label if you need to
if (needToRun == true) {
delete input;
- for (map<string, bool>::iterator itBool = wroteListFile.begin(); itBool != wroteListFile.end(); itBool++) {
- string filename = fileroot + itBool->first;
- if ((itBool->first == "rare") || (itBool->first == "abund")) {
- filename = fileroot + itBool->first + ".list";
- }
- if (itBool->second) { //we wrote to this file
- outputNames.push_back(filename);
- }else{
- remove(filename.c_str());
- }
- }
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
-
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}else { //you are using the namefile to determine abundance
- if (outputDir == "") { outputDir = hasPath(namefile); }
+ if (outputDir == "") { outputDir = m->hasPath(namefile); }
splitNames();
writeNames();
if (accnos) { writeAccnos(tag); }
if (fastafile != "") { parseFasta(tag); }
}
-
+
+ //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("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
string bin = thisList->get(i);
vector<string> names;
- splitAtComma(bin, names); //parses bin into individual sequence names
+ m->splitAtComma(bin, names); //parses bin into individual sequence names
int size = names.size();
if (size <= cutoff) {
}
}//end for
- writeList(thisList);
string tag = thisList->getLabel() + ".";
+
+ writeList(thisList, tag);
+
if (groupfile != "") { parseGroup(tag); }
if (accnos) { writeAccnos(tag); }
if (fastafile != "") { parseFasta(tag); }
}
}
/**********************************************************************************************************************/
-int SplitAbundCommand::writeList(ListVector* thisList) {
+int SplitAbundCommand::writeList(ListVector* thisList, string tag) {
try {
map<string, ofstream*> filehandles;
ofstream aout;
ofstream rout;
- if (rareNames.size() != 0) {
- string rare = outputDir + getRootName(getSimpleName(listfile)) + "rare.list";
- wroteListFile["rare"] = true;
- openOutputFileAppend(rare, rout);
- rout << thisList->getLabel() << '\t' << numRareBins << '\t';
- }
+ string rare = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "rare." + getOutputFileNameTag("list");
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["list"].push_back(rare);
- if (abundNames.size() != 0) {
- string abund = outputDir + getRootName(getSimpleName(listfile)) + "abund.list";
- wroteListFile["abund"] = true;
- openOutputFileAppend(abund, aout);
- aout << thisList->getLabel() << '\t' << numAbundBins << '\t';
- }
+ string abund = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "abund." + getOutputFileNameTag("list");
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["list"].push_back(abund);
+
+ if (rareNames.size() != 0) { rout << thisList->getLabel() << '\t' << numRareBins << '\t'; }
+ if (abundNames.size() != 0) { aout << thisList->getLabel() << '\t' << numAbundBins << '\t'; }
for (int i = 0; i < thisList->getNumBins(); i++) {
if (m->control_pressed) { break; }
string bin = list->get(i);
- int size = getNumNames(bin);
+ int size = m->getNumNames(bin);
if (size <= cutoff) { rout << bin << '\t'; }
else { aout << bin << '\t'; }
}
- if (rareNames.size() != 0) { rout << endl; rout.close(); }
- if (abundNames.size() != 0) { aout << endl; aout.close(); }
-
+ if (rareNames.size() != 0) { rout << endl; }
+ if (abundNames.size() != 0) { aout << endl; }
+
+ rout.close();
+ aout.close();
+
}else{ //parse names by abundance and group
- string fileroot = outputDir + getRootName(getSimpleName(listfile));
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
ofstream* temp;
ofstream* temp2;
- map<string, bool> wroteFile;
+ //map<string, bool> wroteFile;
map<string, ofstream*> filehandles;
map<string, ofstream*>::iterator it3;
temp2 = new ofstream;
filehandles[Groups[i]+".abund"] = temp2;
- openOutputFileAppend(fileroot + Groups[i] + ".rare.list", *(filehandles[Groups[i]+".rare"]));
- openOutputFileAppend(fileroot + Groups[i] + ".abund.list", *(filehandles[Groups[i]+".abund"]));
+ string rareGroupFileName = fileroot + Groups[i] + tag + ".rare." + getOutputFileNameTag("list");
+ string abundGroupFileName = fileroot + Groups[i] + tag + ".abund." + getOutputFileNameTag("list");
+ m->openOutputFile(rareGroupFileName, *(filehandles[Groups[i]+".rare"]));
+ m->openOutputFile(abundGroupFileName, *(filehandles[Groups[i]+".abund"]));
+ outputNames.push_back(rareGroupFileName); outputTypes["list"].push_back(rareGroupFileName);
+ outputNames.push_back(abundGroupFileName); outputTypes["list"].push_back(abundGroupFileName);
}
map<string, string> groupVector;
string bin = list->get(i);
vector<string> names;
- splitAtComma(bin, names); //parses bin into individual sequence names
+ m->splitAtComma(bin, names); //parses bin into individual sequence names
//parse bin into list of sequences in each group
for (int j = 0; j < names.size(); j++) {
string group = groupMap->getGroup(names[j]);
- if (inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
itGroup = groupBins.find(group+rareAbund);
if(itGroup == groupBins.end()) {
groupBins[group+rareAbund] = names[j]; //add first name
//end list vector
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
(*(filehandles[it3->first])) << thisList->getLabel() << '\t' << groupNumBins[it3->first] << '\t' << groupVector[it3->first] << endl; // label numBins listvector for that group
- wroteListFile[it3->first] = true;
(*(filehandles[it3->first])).close();
delete it3->second;
}
//open input file
ifstream in;
- openInputFile(namefile, in);
+ m->openInputFile(namefile, in);
while (!in.eof()) {
if (m->control_pressed) { break; }
string firstCol, secondCol;
- in >> firstCol >> secondCol; gobble(in);
+ in >> firstCol >> secondCol; m->gobble(in);
nameMap[firstCol] = secondCol;
- int size = getNumNames(secondCol);
+ int size = m->getNumNames(secondCol);
if (size <= cutoff) {
rareNames.insert(firstCol);
try {
//open input file
ifstream in;
- openInputFile(namefile, in);
+ m->openInputFile(namefile, in);
while (!in.eof()) {
if (m->control_pressed) { break; }
string firstCol, secondCol;
- in >> firstCol >> secondCol; gobble(in);
+ in >> firstCol >> secondCol; m->gobble(in);
nameMap[firstCol] = secondCol;
}
string bin = thisList->get(i);
vector<string> names;
- splitAtComma(bin, names); //parses bin into individual sequence names
+ m->splitAtComma(bin, names); //parses bin into individual sequence names
for (int j = 0; j < names.size(); j++) { nameMap[names[j]] = names[j]; }
}//end for
ofstream aout;
ofstream rout;
+ string rare = outputDir + m->getRootName(m->getSimpleName(namefile)) + "rare." + getOutputFileNameTag("name");
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["name"].push_back(rare);
+
+ string abund = outputDir + m->getRootName(m->getSimpleName(namefile)) + "abund." + getOutputFileNameTag("name");
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["name"].push_back(abund);
+
if (rareNames.size() != 0) {
- string rare = outputDir + getRootName(getSimpleName(namefile)) + "rare.names";
- openOutputFile(rare, rout);
- outputNames.push_back(rare);
-
for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
rout << (*itRare) << '\t' << nameMap[(*itRare)] << endl;
}
- rout.close();
}
+ rout.close();
if (abundNames.size() != 0) {
- string abund = outputDir + getRootName(getSimpleName(namefile)) + "abund.names";
- openOutputFile(abund, aout);
- outputNames.push_back(abund);
-
for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
aout << (*itAbund) << '\t' << nameMap[(*itAbund)] << endl;
}
- aout.close();
}
-
+ aout.close();
+
}else{ //parse names by abundance and group
- string fileroot = outputDir + getRootName(getSimpleName(namefile));
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(namefile));
ofstream* temp;
ofstream* temp2;
- map<string, bool> wroteFile;
map<string, ofstream*> filehandles;
map<string, ofstream*>::iterator it3;
temp2 = new ofstream;
filehandles[Groups[i]+".abund"] = temp2;
- openOutputFile(fileroot + Groups[i] + ".rare.names", *(filehandles[Groups[i]+".rare"]));
- openOutputFile(fileroot + Groups[i] + ".abund.names", *(filehandles[Groups[i]+".abund"]));
-
- wroteFile[Groups[i] + ".rare"] = false;
- wroteFile[Groups[i] + ".abund"] = false;
+ string rareGroupFileName = fileroot + Groups[i] + ".rare." + getOutputFileNameTag("name");
+ string abundGroupFileName = fileroot + Groups[i] + ".abund." + getOutputFileNameTag("name");
+ m->openOutputFile(rareGroupFileName, *(filehandles[Groups[i]+".rare"]));
+ m->openOutputFile(abundGroupFileName, *(filehandles[Groups[i]+".abund"]));
}
for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
vector<string> names;
- splitAtComma(itName->second, names); //parses bin into individual sequence names
+ m->splitAtComma(itName->second, names); //parses bin into individual sequence names
string rareAbund;
if (rareNames.count(itName->first) != 0) { //you are a rare name
string group = groupMap->getGroup(names[i]);
- if (inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
itout = outputStrings.find(group+rareAbund);
if (itout == outputStrings.end()) {
outputStrings[group+rareAbund] = names[i] + '\t' + names[i];
}
}
- for (itout = outputStrings.begin(); itout != outputStrings.end(); itout++) {
- *(filehandles[itout->first]) << itout->second << endl;
- wroteFile[itout->first] = true;
- }
+ for (itout = outputStrings.begin(); itout != outputStrings.end(); itout++) { *(filehandles[itout->first]) << itout->second << endl; }
}
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
(*(filehandles[it3->first])).close();
- if (wroteFile[it3->first] == true) { outputNames.push_back(fileroot + it3->first + ".names"); }
- else { remove((it3->first).c_str()); }
+ outputNames.push_back(fileroot + it3->first + "." + getOutputFileNameTag("name")); outputTypes["name"].push_back(fileroot + it3->first + "." + getOutputFileNameTag("name"));
delete it3->second;
}
}
ofstream aout;
ofstream rout;
- if (rareNames.size() != 0) {
- string rare = outputDir + getRootName(getSimpleName(inputFile)) + tag + "rare.accnos";
- openOutputFile(rare, rout);
- outputNames.push_back(rare);
-
- for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
- rout << (*itRare) << endl;
- }
- rout.close();
+
+ string rare = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag + "rare." + getOutputFileNameTag("accnos");
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["accnos"].push_back(rare);
+
+ for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
+ rout << (*itRare) << endl;
}
+ rout.close();
+
+ string abund = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag + "abund." + getOutputFileNameTag("accnos");
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["accnos"].push_back(abund);
- if (abundNames.size() != 0) {
- string abund = outputDir + getRootName(getSimpleName(inputFile)) + tag + "abund.accnos";
- openOutputFile(abund, aout);
- outputNames.push_back(abund);
-
- for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
- aout << (*itAbund) << endl;
- }
- aout.close();
+ for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
+ aout << (*itAbund) << endl;
}
+ aout.close();
+
}else{ //parse names by abundance and group
- string fileroot = outputDir + getRootName(getSimpleName(inputFile));
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(inputFile));
ofstream* temp;
ofstream* temp2;
- map<string, bool> wroteFile;
map<string, ofstream*> filehandles;
map<string, ofstream*>::iterator it3;
temp2 = new ofstream;
filehandles[Groups[i]+".abund"] = temp2;
- openOutputFile(fileroot + tag + Groups[i] + ".rare.accnos", *(filehandles[Groups[i]+".rare"]));
- openOutputFile(fileroot + tag + Groups[i] + ".abund.accnos", *(filehandles[Groups[i]+".abund"]));
-
- wroteFile[Groups[i] + ".rare"] = false;
- wroteFile[Groups[i] + ".abund"] = false;
+ m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("accnos"), *(filehandles[Groups[i]+".rare"]));
+ m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("accnos"), *(filehandles[Groups[i]+".abund"]));
}
//write rare
for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
string group = groupMap->getGroup(*itRare);
- if (inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
*(filehandles[group+".rare"]) << *itRare << endl;
- wroteFile[group+".rare"] = true;
}
}
for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
string group = groupMap->getGroup(*itAbund);
- if (inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
*(filehandles[group+".abund"]) << *itAbund << endl;
- wroteFile[group+".abund"] = true;
}
}
//close files
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
(*(filehandles[it3->first])).close();
- if (wroteFile[it3->first] == true) { outputNames.push_back(fileroot + tag + it3->first + ".accnos"); }
- else { remove((fileroot + tag + it3->first + ".accnos").c_str()); }
+ outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("accnos")); outputTypes["accnos"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("accnos"));
delete it3->second;
}
}
ofstream aout;
ofstream rout;
- if (rareNames.size() != 0) {
- string rare = outputDir + getRootName(getSimpleName(groupfile)) + tag + "rare.groups";
- openOutputFile(rare, rout);
- outputNames.push_back(rare);
- }
+ string rare = outputDir + m->getRootName(m->getSimpleName(groupfile)) + tag + "rare." + getOutputFileNameTag("group");
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["group"].push_back(rare);
+
+ string abund = outputDir + m->getRootName(m->getSimpleName(groupfile)) + tag + "abund." + getOutputFileNameTag("group");
+;
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["group"].push_back(abund);
- if (abundNames.size() != 0) {
- string abund = outputDir + getRootName(getSimpleName(groupfile)) + tag + "abund.groups";
- openOutputFile(abund, aout);
- outputNames.push_back(abund);
- }
-
-
for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
vector<string> names;
- splitAtComma(itName->second, names); //parses bin into individual sequence names
+ m->splitAtComma(itName->second, names); //parses bin into individual sequence names
for (int i = 0; i < names.size(); i++) {
}
}
- if (rareNames.size() != 0) { rout.close(); }
- if (abundNames.size() != 0) { aout.close(); }
+ rout.close();
+ aout.close();
}else{ //parse names by abundance and group
- string fileroot = outputDir + getRootName(getSimpleName(groupfile));
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(groupfile));
ofstream* temp;
ofstream* temp2;
- map<string, bool> wroteFile;
map<string, ofstream*> filehandles;
map<string, ofstream*>::iterator it3;
temp2 = new ofstream;
filehandles[Groups[i]+".abund"] = temp2;
- openOutputFile(fileroot + tag + Groups[i] + ".rare.groups", *(filehandles[Groups[i]+".rare"]));
- openOutputFile(fileroot + tag + Groups[i] + ".abund.groups", *(filehandles[Groups[i]+".abund"]));
-
- wroteFile[Groups[i] + ".rare"] = false;
- wroteFile[Groups[i] + ".abund"] = false;
+ m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("group"), *(filehandles[Groups[i]+".rare"]));
+ m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("group"), *(filehandles[Groups[i]+".abund"]));
}
for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
vector<string> names;
- splitAtComma(itName->second, names); //parses bin into individual sequence names
+ m->splitAtComma(itName->second, names); //parses bin into individual sequence names
string rareAbund;
if (rareNames.count(itName->first) != 0) { //you are a rare name
string group = groupMap->getGroup(names[i]);
- if (inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
*(filehandles[group+rareAbund]) << names[i] << '\t' << group << endl;
- wroteFile[group+rareAbund] = true;
}
}
}
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
(*(filehandles[it3->first])).close();
- if (wroteFile[it3->first] == true) { outputNames.push_back(fileroot + tag + it3->first + ".groups"); }
- else { remove((fileroot + tag + it3->first + ".groups").c_str()); }
+ outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("group")); outputTypes["group"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("group"));
delete it3->second;
}
}
ofstream aout;
ofstream rout;
- if (rareNames.size() != 0) {
- string rare = outputDir + getRootName(getSimpleName(fastafile)) + tag + "rare.fasta";
- openOutputFile(rare, rout);
- outputNames.push_back(rare);
- }
-
- if (abundNames.size() != 0) {
- string abund = outputDir + getRootName(getSimpleName(fastafile)) + tag + "abund.fasta";
- openOutputFile(abund, aout);
- outputNames.push_back(abund);
- }
-
-
+ string rare = outputDir + m->getRootName(m->getSimpleName(fastafile)) + tag + "rare." + getOutputFileNameTag("fasta");
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["fasta"].push_back(rare);
+
+ string abund = outputDir + m->getRootName(m->getSimpleName(fastafile)) + tag + "abund." + getOutputFileNameTag("fasta");
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["fasta"].push_back(abund);
+
//open input file
ifstream in;
- openInputFile(fastafile, in);
+ m->openInputFile(fastafile, in);
while (!in.eof()) {
if (m->control_pressed) { break; }
- Sequence seq(in); gobble(in);
+ Sequence seq(in); m->gobble(in);
if (seq.getName() != "") {
}
}
in.close();
- if (rareNames.size() != 0) { rout.close(); }
- if (abundNames.size() != 0) { aout.close(); }
+ rout.close();
+ aout.close();
}else{ //parse names by abundance and group
- string fileroot = outputDir + getRootName(getSimpleName(fastafile));
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
ofstream* temp;
ofstream* temp2;
- map<string, bool> wroteFile;
map<string, ofstream*> filehandles;
map<string, ofstream*>::iterator it3;
temp2 = new ofstream;
filehandles[Groups[i]+".abund"] = temp2;
- openOutputFile(fileroot + tag + Groups[i] + ".rare.fasta", *(filehandles[Groups[i]+".rare"]));
- openOutputFile(fileroot + tag + Groups[i] + ".abund.fasta", *(filehandles[Groups[i]+".abund"]));
-
- wroteFile[Groups[i] + ".rare"] = false;
- wroteFile[Groups[i] + ".abund"] = false;
+ m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("fasta"), *(filehandles[Groups[i]+".rare"]));
+ m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("fasta"), *(filehandles[Groups[i]+".abund"]));
}
//open input file
ifstream in;
- openInputFile(fastafile, in);
+ m->openInputFile(fastafile, in);
while (!in.eof()) {
if (m->control_pressed) { break; }
- Sequence seq(in); gobble(in);
+ Sequence seq(in); m->gobble(in);
if (seq.getName() != "") {
map<string, string>::iterator itNames = nameMap.find(seq.getName());
m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine();
}else{
vector<string> names;
- splitAtComma(itNames->second, names); //parses bin into individual sequence names
+ m->splitAtComma(itNames->second, names); //parses bin into individual sequence names
string rareAbund;
if (rareNames.count(itNames->first) != 0) { //you are a rare name
string group = groupMap->getGroup(seq.getName());
- if (inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
seq.printSequence(*(filehandles[group+rareAbund]));
- wroteFile[group+rareAbund] = true;
}else if(group == "not found") {
m->mothurOut(seq.getName() + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
}
for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
(*(filehandles[it3->first])).close();
- if (wroteFile[it3->first] == true) { outputNames.push_back(fileroot + tag + it3->first + ".fasta"); }
- else { remove((fileroot + tag + it3->first + ".fasta").c_str()); }
+ outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("fasta")); outputTypes["fasta"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("fasta"));
delete it3->second;
}
}
projects / mothur.git / blobdiff