*/
#include "splitabundcommand.h"
+#include "sharedutilities.h"
+//**********************************************************************************************************************
+vector<string> SplitAbundCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,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", "none", "none","count",false,false); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); 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, count, cutoff, group, label, groups, cutoff and accnos.\n";
+ helpString += "The fasta and a list or name or count 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::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],[tag],[tag2],fasta-[filename],[tag],[group],[tag2],fasta"; }
+ else if (type == "list") { pattern = "[filename],[tag],[tag2],list-[filename],[group],[tag],[tag2],list"; }
+ else if (type == "name") { pattern = "[filename],[tag],names-[filename],[group],[tag],names"; }
+ else if (type == "count") { pattern = "[filename],[tag],[tag2],count_table-[filename],[tag],count_table"; }
+ else if (type == "group") { pattern = "[filename],[tag],[tag2],groups-[filename],[tag],[group],[tag2],groups"; }
+ else if (type == "accnos") { pattern = "[filename],[tag],[tag2],accnos-[filename],[tag],[group],[tag2],accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SplitAbundCommand::SplitAbundCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = 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;
- wroteRareList = false;
- wroteAbundList = 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[] = {"list","name","group","label","accnos","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;
+ outputTypes["count"] = 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 = 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; }
}
+ 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
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
- else if (listfile == "not found") { listfile = ""; }
+ else if (listfile == "not found") { listfile = ""; }
+ else{ inputFile = listfile; m->setListFile(listfile); }
- //check for required parameters
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { 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->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") { abort = true; }
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else {
- groupMap = new GroupMap(groupfile);
-
- int error = groupMap->readMap();
+ int error = groupMap.readMap(groupfile);
if (error == 1) { abort = true; }
+ m->setGroupFile(groupfile);
}
- //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 != "")) { m->mothurOut("You must either a listfile or a namefile for the split.abund command, but NOT BOTH. "); m->mothurOutEndLine(); abort = true; }
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else {
+ m->setCountTableFile(countfile);
+ ct.readTable(countfile, true);
+ }
+
+ 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;
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else { m->splitAtDash(groups, Groups); }
+
+ if (((groupfile == "") && (countfile == ""))&& (groups != "")) { m->mothurOut("You cannot select groups without a valid group or count file, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = ""; Groups.clear(); }
+ if (countfile != "") {
+ if (!ct.hasGroupInfo()) { m->mothurOut("You cannot pick groups without group info in your count file; I will disregard your groups selection."); m->mothurOutEndLine(); groups = ""; Groups.clear(); }
+ }
+
+ //do you have all files needed
+ if ((listfile == "") && (namefile == "") && (countfile == "")) {
+ 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 {
+ countfile = m->getCountTableFile();
+ if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current list, count or namefile and one 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 list or a names file splits the sequences into rare and abundant groups.. \n");
- m->mothurOut("The split.abund command parameters are list, name, cutoff, group, label and accnos.\n");
- m->mothurOut("The list or name parameter is 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 split.abund command should be used in the following format: split.abund(list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n");
- m->mothurOut("Example: split.abundt(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; }
-}
+SplitAbundCommand::~SplitAbundCommand(){}
//**********************************************************************************************************************
int SplitAbundCommand::execute(){
try {
- if (abort == true) { return 0; }
-
- if (namefile != "") { split(); }
- else {
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ if (Groups.size() != 0) {
+ vector<string> allGroups;
+ if (countfile != "") { allGroups = ct.getNamesOfGroups(); }
+ else { allGroups = groupMap.getNamesOfGroups(); }
+ SharedUtil util;
+ util.setGroups(Groups, allGroups);
+ }
- //remove old files so you can append later....
- string fileroot = outputDir + getRootName(getSimpleName(listfile));
- remove((fileroot + "rare.list").c_str());
- remove((fileroot + "abund.list").c_str());
+ if (listfile != "") { //you are using a listfile to determine abundance
+ 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;
set<string> userLabels = labels;
- input = new InputData(listfile, "list");
- list = input->getListVector();
+ InputData input(listfile, "list");
+ ListVector* list = input.getListVector();
string lastLabel = list->getLabel();
- if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ //do you have a namefile or do we need to similate one?
+ if (namefile != "") { readNamesFile(); }
+ else { createNameMap(list); }
+
+ if (m->control_pressed) { 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 list; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if(allLines == 1 || labels.count(list->getLabel()) == 1){
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
- split(list);
+ splitList(list);
processedLabels.insert(list->getLabel());
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(lastLabel); //get new list vector to process
+ list = input.getListVector(lastLabel); //get new list vector to process
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
- split(list);
+ splitList(list);
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
lastLabel = list->getLabel();
delete list;
- list = input->getListVector(); //get new list vector to process
+ 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) { 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) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//run last label if you need to
if (needToRun == true) {
if (list != NULL) { delete list; }
- list = input->getListVector(lastLabel); //get new list vector to process
+ list = input.getListVector(lastLabel); //get new list vector to process
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
- split(list);
+ splitList(list);
delete list;
}
- delete input;
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ }else if (namefile != "") { //you are using the namefile to determine abundance
+ if (outputDir == "") { outputDir = m->hasPath(namefile); }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ splitNames();
+ writeNames();
- if (wroteAbundList) { outputNames.push_back(fileroot + "abund.list"); }
- if (wroteRareList) { outputNames.push_back(fileroot + "rare.list"); }
+ string tag = "";
+ if (groupfile != "") { parseGroup(tag); }
+ if (accnos) { writeAccnos(tag); }
+ if (fastafile != "") { parseFasta(tag); }
+ }else {
+ //split by countfile
+ string tag = "";
+ splitCount();
+
+ 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); }
+ }
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}
}
/**********************************************************************************************************************/
-int SplitAbundCommand::split(ListVector* thisList) {
+int SplitAbundCommand::splitList(ListVector* thisList) {
try {
-
- SAbundVector* sabund = new SAbundVector();
- *sabund = thisList->getSAbundVector();
-
- //find out how many bins are rare and how many are abundant so you can process the list vector one bin at a time
- // and don't have to store the bins until you are done with the whole vector, this save alot of space.
- int numRareBins = 0;
- for (int i = 0; i <= sabund->getMaxRank(); i++) {
- if (i > cutoff) { break; }
- numRareBins += sabund->get(i);
- }
- int numAbundBins = thisList->getNumBins() - numRareBins;
- delete sabund;
-
- //setup output files
- ofstream outListAbund;
- ofstream outListRare;
- ofstream outGroupRare;
- ofstream outGroupAbund;
- ofstream outAccnosRare;
- ofstream outAccnosAbund;
-
- string fileroot = outputDir + getRootName(getSimpleName(listfile));
- if (numRareBins > 0) {
- wroteRareList = true;
- string listRareName = fileroot + "rare.list";
- openOutputFileAppend(listRareName, outListRare);
- outListRare << thisList->getLabel() << '\t' << numRareBins << '\t';
-
- if (accnos) {
- string accnosName = fileroot + thisList->getLabel() + ".rare.accnos";
- openOutputFile(accnosName, outAccnosRare);
- outputNames.push_back(accnosName);
- }
-
- if (groupfile != "") {
- string groupFileName = outputDir + getRootName(getSimpleName(groupfile)) + thisList->getLabel() + ".rare.group";
- openOutputFile(groupFileName, outGroupRare);
- outputNames.push_back(groupFileName);
- }
- }
+ rareNames.clear();
+ abundNames.clear();
- if (numAbundBins > 0) {
- wroteAbundList = true;
- string listAbundName = fileroot + "abund.list";
- openOutputFileAppend(listAbundName, outListAbund);
- outListAbund << thisList->getLabel() << '\t' << numAbundBins << '\t';
+ //get rareNames and abundNames
+ int numRareBins = 0;
+ for (int i = 0; i < thisList->getNumBins(); i++) {
+ if (m->control_pressed) { return 0; }
- if (accnos) {
- string accnosName = fileroot + thisList->getLabel() + ".abund.accnos";
- openOutputFile(accnosName, outAccnosAbund);
- outputNames.push_back(accnosName);
+ string bin = thisList->get(i);
+
+ vector<string> names;
+ m->splitAtComma(bin, names); //parses bin into individual sequence names
+ int size = names.size();
+
+ //if countfile is not blank we assume the list file is unique, otherwise we assume it includes all seqs
+ if (countfile != "") {
+ size = 0;
+ for (int j = 0; j < names.size(); j++) { size += ct.getNumSeqs(names[j]); }
+ }
+
+ if (size <= cutoff) {
+ numRareBins++;
+ for (int j = 0; j < names.size(); j++) { rareNames.insert(names[j]); }
+ }else{
+ for (int j = 0; j < names.size(); j++) { abundNames.insert(names[j]); }
}
+ }//end for
+
+
+ string tag = thisList->getLabel();
+
+ writeList(thisList, tag, numRareBins);
+
+ if (groupfile != "") { parseGroup(tag); }
+ if (accnos) { writeAccnos(tag); }
+ if (fastafile != "") { parseFasta(tag); }
+ if (countfile != "") { parseCount(tag); }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "splitList");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::writeList(ListVector* thisList, string tag, int numRareBins) {
+ try {
+
+ map<string, ofstream*> filehandles;
+
+ if (Groups.size() == 0) {
+ int numAbundBins = thisList->getNumBins() - numRareBins;
+
+ ofstream aout;
+ ofstream rout;
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ string rare = getOutputFileName("list",variables);
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["list"].push_back(rare);
+
+ variables["[tag2]"] = "abund";
+ string abund = getOutputFileName("list",variables);
+ 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 = thisList->get(i);
+ vector<string> names;
+ m->splitAtComma(bin, names);
+
+ int size = names.size();
+ if (countfile != "") {
+ size = 0;
+ for (int j = 0; j < names.size(); j++) { size += ct.getNumSeqs(names[j]); }
+ }
- if (groupfile != "") {
- string groupFileName = outputDir + getRootName(getSimpleName(groupfile)) + thisList->getLabel() + ".abund.group";
- openOutputFile(groupFileName, outGroupAbund);
- outputNames.push_back(groupFileName);
+ if (size <= cutoff) { rout << bin << '\t'; }
+ else { aout << bin << '\t'; }
}
- }
-
- for (int i = 0; i < thisList->getNumBins(); i++) {
- if (m->control_pressed) { break; }
- string bin = list->get(i);
+ if (rareNames.size() != 0) { rout << endl; }
+ if (abundNames.size() != 0) { aout << endl; }
+
+ rout.close();
+ aout.close();
- int size = getNumNames(bin);
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
+ ofstream* temp;
+ ofstream* temp2;
+ //map<string, bool> wroteFile;
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+ for (int i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[Groups[i]+".rare"] = temp;
+ temp2 = new ofstream;
+ filehandles[Groups[i]+".abund"] = temp2;
+
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ variables["[group]"] = Groups[i];
+ string rareGroupFileName = getOutputFileName("list",variables);
+ variables["[tag2]"] = "abund";
+ string abundGroupFileName = getOutputFileName("list",variables);
+ 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);
+ }
- if (size <= cutoff) { outListRare << bin << '\t'; }
- else { outListAbund << bin << '\t'; }
+ map<string, string> groupVector;
+ map<string, string>::iterator itGroup;
+ map<string, int> groupNumBins;
+
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ groupNumBins[it3->first] = 0;
+ groupVector[it3->first] = "";
+ }
+
+ for (int i = 0; i < thisList->getNumBins(); i++) {
+ if (m->control_pressed) { break; }
+
+ map<string, string> groupBins;
+ string bin = thisList->get(i);
- if ((groupfile != "") || (accnos)) { //you need to parse the bin...
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++) {
-
- //write to accnos file
- if (accnos) {
- if (size <= cutoff) { outAccnosRare << names[j] << endl; }
- else { outAccnosAbund << names[j] << endl; }
- }
-
- //write to groupfile
- if (groupfile != "") {
- string group = groupMap->getGroup(names[j]);
-
- if (group == "not found") { //error in groupfile so close and remove output file and disregard groupfile
- m->mothurOut(names[j] + " is not in your groupfile. disregarding groupfile."); m->mothurOutEndLine();
- delete groupMap;
- if (numAbundBins > 0) {
- outGroupAbund.close();
- remove((outputDir + getRootName(getSimpleName(groupfile)) + thisList->getLabel() + ".abund.group").c_str());
- }
- if (numRareBins > 0) {
- outGroupRare.close();
- remove((outputDir + getRootName(getSimpleName(groupfile)) + thisList->getLabel() + ".rare.group").c_str());
- }
- groupfile = "";
- }else {
- if (size <= cutoff) { outGroupRare << names[j] << '\t' << group << endl; }
- else { outGroupAbund << names[j] << '\t' << group << endl; }
- }
+ string rareAbund;
+ if (rareNames.count(names[j]) != 0) { //you are a rare name
+ rareAbund = ".rare";
+ }else{ //you are a abund name
+ rareAbund = ".abund";
}
- }//end for names
- }//end if parse
- }//end for list
-
-
- //close files
- if (numRareBins > 0) {
- outListRare << endl;
- outListRare.close();
- if (accnos) { outAccnosRare.close(); }
- if (groupfile != "") { outGroupRare.close(); }
+ if (countfile == "") {
+ string group = groupMap.getGroup(names[j]);
+
+ 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
+ groupNumBins[group+rareAbund]++;
+ }else{ //add another name
+ groupBins[group+rareAbund] += "," + names[j];
+ }
+ }else if(group == "not found") {
+ m->mothurOut(names[j] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
+ }
+ }else {
+ vector<string> thisSeqsGroups = ct.getGroups(names[j]);
+ for (int k = 0; k < thisSeqsGroups.size(); k++) {
+ if (m->inUsersGroups(thisSeqsGroups[k], Groups)) { //only add if this is in a group we want
+ itGroup = groupBins.find(thisSeqsGroups[k]+rareAbund);
+ if(itGroup == groupBins.end()) {
+ groupBins[thisSeqsGroups[k]+rareAbund] = names[j]; //add first name
+ groupNumBins[thisSeqsGroups[k]+rareAbund]++;
+ }else{ //add another name
+ groupBins[thisSeqsGroups[k]+rareAbund] += "," + names[j];
+ }
+ }
+ }
+ }
+ }
+
+
+ for (itGroup = groupBins.begin(); itGroup != groupBins.end(); itGroup++) {
+ groupVector[itGroup->first] += itGroup->second + '\t';
+ }
+ }
+
+ //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
+ (*(filehandles[it3->first])).close();
+ delete it3->second;
+ }
}
- if (numAbundBins > 0) {
- outListAbund << endl;
- outListAbund.close();
- if (accnos) { outAccnosAbund.close(); }
- if (groupfile != "") { outGroupAbund.close(); }
- }
-
return 0;
}
catch(exception& e) {
- m->errorOut(e, "SplitAbundCommand", "split");
+ m->errorOut(e, "SplitAbundCommand", "writeList");
exit(1);
}
}
/**********************************************************************************************************************/
-int SplitAbundCommand::split() { //namefile
+int SplitAbundCommand::splitCount() { //countfile
try {
- //setup output files
- ofstream outNameAbund;
- ofstream outNameRare;
- ofstream outGroupRare;
- ofstream outGroupAbund;
- ofstream outAccnosRare;
- ofstream outAccnosAbund;
-
- bool wroteNameAbund = false;
- bool wroteNameRare = false;
- bool wroteGroupRare = false;
- bool wroteGroupAbund = false;
- bool wroteAccnosRare = false;
- bool wroteAccnosAbund = false;
-
- //prepare output files
- string fileroot = outputDir + getRootName(getSimpleName(namefile));
-
- string nameRareName = fileroot + "rare.names";
- openOutputFile(nameRareName, outNameRare);
- string nameAbundName = fileroot + "abund.names";
- openOutputFile(nameAbundName, outNameAbund);
-
- if (accnos) {
- string accnosName = fileroot + "rare.accnos";
- openOutputFile(accnosName, outAccnosRare);
-
- accnosName = fileroot + "abund.accnos";
- openOutputFile(accnosName, outAccnosAbund);
+ rareNames.clear();
+ abundNames.clear();
+
+ vector<string> allNames = ct.getNamesOfSeqs();
+ for (int i = 0; i < allNames.size(); i++) {
+
+ if (m->control_pressed) { return 0; }
+
+ int size = ct.getNumSeqs(allNames[i]);
+ nameMap[allNames[i]] = allNames[i];
+
+ if (size <= cutoff) {
+ rareNames.insert(allNames[i]);
+ }else{
+ abundNames.insert(allNames[i]);
+ }
}
+
+ //write out split count files
+ parseCount("");
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "splitCount");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::splitNames() { //namefile
+ try {
+
+ rareNames.clear();
+ abundNames.clear();
- if (groupfile != "") {
- string groupFileName = outputDir + getRootName(getSimpleName(groupfile)) + ".rare.group";
- openOutputFile(groupFileName, outGroupRare);
+ //open input file
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; m->gobble(in);
- groupFileName = outputDir + getRootName(getSimpleName(groupfile)) + ".abund.group";
- openOutputFile(groupFileName, outGroupAbund);
+ nameMap[firstCol] = secondCol;
+
+ int size = m->getNumNames(secondCol);
+
+ if (size <= cutoff) {
+ rareNames.insert(firstCol);
+ }else{
+ abundNames.insert(firstCol);
+ }
}
-
-
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "splitNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::readNamesFile() {
+ 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);
- int size = getNumNames(secondCol);
+ nameMap[firstCol] = secondCol;
+ }
+ in.close();
- if (size <= cutoff) { outNameRare << firstCol << '\t' << secondCol << endl; wroteNameRare = true; }
- else { outNameAbund << firstCol << '\t' << secondCol << endl; wroteNameAbund = true; }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "readNamesFile");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::createNameMap(ListVector* thisList) {
+ try {
+
+ if (thisList != NULL) {
+ for (int i = 0; i < thisList->getNumBins(); i++) {
+ if (m->control_pressed) { return 0; }
+
+ string bin = thisList->get(i);
+
+ vector<string> 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
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "createNameMap");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::parseCount(string tag) { //namefile
+ try {
+
+ map<string, ofstream*> filehandles;
+
+ if (Groups.size() == 0) {
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ string rare = getOutputFileName("count",variables);
+ outputNames.push_back(rare); outputTypes["count"].push_back(rare);
+ variables["[tag2]"] = "abund";
+ string abund = getOutputFileName("count",variables);
+ outputNames.push_back(abund); outputTypes["count"].push_back(abund);
+
+ CountTable rareTable;
+ CountTable abundTable;
+ if (ct.hasGroupInfo()) {
+ vector<string> ctGroups = ct.getNamesOfGroups();
+ for (int i = 0; i < ctGroups.size(); i++) { rareTable.addGroup(ctGroups[i]); abundTable.addGroup(ctGroups[i]); }
+ }
+
+ if (rareNames.size() != 0) {
+ for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
+ if (ct.hasGroupInfo()) {
+ vector<int> groupCounts = ct.getGroupCounts(*itRare);
+ rareTable.push_back(*itRare, groupCounts);
+ }else {
+ int groupCounts = ct.getNumSeqs(*itRare);
+ rareTable.push_back(*itRare, groupCounts);
+ }
+ }
+ if (rareTable.hasGroupInfo()) {
+ vector<string> ctGroups = rareTable.getNamesOfGroups();
+ for (int i = 0; i < ctGroups.size(); i++) {
+ if (rareTable.getGroupCount(ctGroups[i]) == 0) { rareTable.removeGroup(ctGroups[i]); }
+ }
+ }
+ rareTable.printTable(rare);
+ }
+
+
+ if (abundNames.size() != 0) {
+ for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
+ if (ct.hasGroupInfo()) {
+ vector<int> groupCounts = ct.getGroupCounts(*itAbund);
+ abundTable.push_back(*itAbund, groupCounts);
+ }else {
+ int groupCounts = ct.getNumSeqs(*itAbund);
+ abundTable.push_back(*itAbund, groupCounts);
+ }
+ }
+ if (abundTable.hasGroupInfo()) {
+ vector<string> ctGroups = abundTable.getNamesOfGroups();
+ for (int i = 0; i < ctGroups.size(); i++) {
+ if (abundTable.getGroupCount(ctGroups[i]) == 0) { abundTable.removeGroup(ctGroups[i]); }
+ }
+ }
+ abundTable.printTable(abund);
+ }
+
+ }else{ //parse names by abundance and group
+ map<string, CountTable*> countTableMap;
+ map<string, CountTable*>::iterator it3;
+
+ for (int i=0; i<Groups.size(); i++) {
+ CountTable* rareCt = new CountTable();
+ rareCt->addGroup(Groups[i]);
+ countTableMap[Groups[i]+".rare"] = rareCt;
+ CountTable* abundCt = new CountTable();
+ abundCt->addGroup(Groups[i]);
+ countTableMap[Groups[i]+".abund"] = abundCt;
+ }
+
+ vector<string> allNames = ct.getNamesOfSeqs();
+ for (int i = 0; i < allNames.size(); i++) {
+ string rareAbund;
+ if (rareNames.count(allNames[i]) != 0) { //you are a rare name
+ rareAbund = ".rare";
+ }else{ //you are a abund name
+ rareAbund = ".abund";
+ }
+
+ vector<string> thisSeqsGroups = ct.getGroups(allNames[i]);
+ for (int j = 0; j < thisSeqsGroups.size(); j++) {
+ if (m->inUsersGroups(thisSeqsGroups[j], Groups)) { //only add if this is in a group we want
+ int num = ct.getGroupCount(allNames[i], thisSeqsGroups[j]);
+ vector<int> nums; nums.push_back(num);
+ countTableMap[thisSeqsGroups[j]+rareAbund]->push_back(allNames[i], nums);
+ }
+ }
+ }
+
+
+ for (it3 = countTableMap.begin(); it3 != countTableMap.end(); it3++) {
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(countfile));
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = it3->first;
+ string filename = getOutputFileName("count",variables);
+ outputNames.push_back(filename); outputTypes["count"].push_back(filename);
+ (it3->second)->printTable(filename);
+ delete it3->second;
+ }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "parseCount");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::writeNames() { //namefile
+ try {
+
+ map<string, ofstream*> filehandles;
+
+ if (Groups.size() == 0) {
+ ofstream aout;
+ ofstream rout;
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[tag]"] = "rare";
+ string rare = getOutputFileName("name", variables);
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["name"].push_back(rare);
+
+ variables["[tag]"] = "abund";
+ string abund = getOutputFileName("name", variables);
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["name"].push_back(abund);
+
+ if (rareNames.size() != 0) {
+ for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
+ rout << (*itRare) << '\t' << nameMap[(*itRare)] << endl;
+ }
+ }
+ rout.close();
- if ((groupfile != "") || (accnos)) { //you need to parse the bin...
+ if (abundNames.size() != 0) {
+ for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
+ aout << (*itAbund) << '\t' << nameMap[(*itAbund)] << endl;
+ }
+ }
+ aout.close();
+
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(namefile));
+ ofstream* temp;
+ ofstream* temp2;
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+ for (int i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[Groups[i]+".rare"] = temp;
+ temp2 = new ofstream;
+ filehandles[Groups[i]+".abund"] = temp2;
+
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = "rare";
+ variables["[group]"] = Groups[i];
+ string rareGroupFileName = getOutputFileName("name",variables);
+ variables["[tag]"] = "abund";
+ string abundGroupFileName = getOutputFileName("name",variables);
+ 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(secondCol, names); //parses bin into individual sequence names
+ m->splitAtComma(itName->second, 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 rareAbund;
+ if (rareNames.count(itName->first) != 0) { //you are a rare name
+ rareAbund = ".rare";
+ }else{ //you are a abund name
+ rareAbund = ".abund";
+ }
+
+ map<string, string> outputStrings;
+ map<string, string>::iterator itout;
+ for (int i = 0; i < names.size(); i++) {
- //write to accnos file
- if (accnos) {
- if (size <= cutoff) { outAccnosRare << names[j] << endl; wroteAccnosRare = true; }
- else { outAccnosAbund << names[j] << endl; wroteAccnosAbund = true; }
- }
+ string group = groupMap.getGroup(names[i]);
- //write to groupfile
- if (groupfile != "") {
- string group = groupMap->getGroup(names[j]);
+ 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];
+ }else { outputStrings[group+rareAbund] += "," + names[i]; }
+ }else if(group == "not found") {
+ m->mothurOut(names[i] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
+ }
+ }
+
+ 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();
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = it3->first;
+ outputNames.push_back(getOutputFileName("name",variables)); outputTypes["name"].push_back(getOutputFileName("name",variables));
+ delete it3->second;
+ }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "writeNames");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+//just write the unique names - if a namesfile is given
+int SplitAbundCommand::writeAccnos(string tag) {
+ try {
+
+ map<string, ofstream*> filehandles;
+
+ if (Groups.size() == 0) {
+ ofstream aout;
+ ofstream rout;
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFile));
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ string rare = getOutputFileName("accnos",variables);
+ 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();
+
+ variables["[tag2]"] = "abund";
+ string abund = getOutputFileName("accnos",variables);
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["accnos"].push_back(abund);
+
+ 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 + m->getRootName(m->getSimpleName(inputFile));
+ ofstream* temp;
+ ofstream* temp2;
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+ for (int i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[Groups[i]+".rare"] = temp;
+ temp2 = new ofstream;
+ filehandles[Groups[i]+".abund"] = temp2;
+
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ variables["[group]"] = Groups[i];
+ m->openOutputFile(getOutputFileName("accnos",variables), *(filehandles[Groups[i]+".rare"]));
+ variables["[tag2]"] = "abund";
+ m->openOutputFile(getOutputFileName("accnos",variables), *(filehandles[Groups[i]+".abund"]));
+ }
+
+ //write rare
+ for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
+ string group = groupMap.getGroup(*itRare);
- if (group == "not found") { //error in groupfile so close and remove output file and disregard groupfile
- m->mothurOut(names[j] + " is not in your groupfile. disregarding groupfile."); m->mothurOutEndLine();
- delete groupMap;
-
- outGroupAbund.close();
- remove((outputDir + getRootName(getSimpleName(groupfile)) + ".abund.group").c_str());
- outGroupRare.close();
- remove((outputDir + getRootName(getSimpleName(groupfile)) + ".rare.group").c_str());
-
- groupfile = "";
- wroteGroupRare = false;
- wroteGroupAbund = false;
- }else {
- if (size <= cutoff) { outGroupRare << names[j] << '\t' << group << endl; wroteGroupRare = true; }
- else { outGroupAbund << names[j] << '\t' << group << endl; wroteGroupAbund = true; }
- }
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ *(filehandles[group+".rare"]) << *itRare << endl;
}
+ }
+
+ //write abund
+ for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
+ string group = groupMap.getGroup(*itAbund);
- }//end for names
- }//end if parse
- }//end while
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ *(filehandles[group+".abund"]) << *itAbund << endl;
+ }
+ }
+
+ //close files
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(filehandles[it3->first])).close();
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = it3->first;
+ outputNames.push_back(getOutputFileName("accnos",variables)); outputTypes["accnos"].push_back(getOutputFileName("accnos",variables));
+ delete it3->second;
+ }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "writeAccnos");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::parseGroup(string tag) { //namefile
+ try {
+ map<string, ofstream*> filehandles;
+
+ if (Groups.size() == 0) {
+ ofstream aout;
+ ofstream rout;
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ string rare = getOutputFileName("group",variables);
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["group"].push_back(rare);
- //close files
- in.close();
- outNameRare.close();
- outNameAbund.close();
- if (!wroteNameRare) { remove((fileroot + "rare.names").c_str()); }
- else { outputNames.push_back((fileroot + "rare.names")); }
- if (!wroteNameAbund) { remove((fileroot + "abund.names").c_str()); }
- else { outputNames.push_back((fileroot + "abund.names")); }
-
- if (groupfile != "") {
- outGroupRare.close(); outGroupAbund.close();
- if (!wroteGroupRare) { remove((outputDir + getRootName(getSimpleName(groupfile)) + ".rare.group").c_str()); }
- else { outputNames.push_back((outputDir + getRootName(getSimpleName(groupfile)) + ".rare.group")); }
- if (!wroteGroupAbund) { remove((outputDir + getRootName(getSimpleName(groupfile)) + ".abund.group").c_str()); }
- else { outputNames.push_back((outputDir + getRootName(getSimpleName(groupfile)) + ".abund.group")); }
+ variables["[tag2]"] = "abund";
+ string abund = getOutputFileName("group",variables);
+;
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["group"].push_back(abund);
+
+ for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
+ vector<string> names;
+ m->splitAtComma(itName->second, names); //parses bin into individual sequence names
+
+ for (int i = 0; i < names.size(); i++) {
+
+ string group = groupMap.getGroup(names[i]);
+
+ if (group == "not found") {
+ m->mothurOut(names[i] + " is not in your groupfile, ignoring, please correct."); m->mothurOutEndLine();
+ }else {
+ if (rareNames.count(itName->first) != 0) { //you are a rare name
+ rout << names[i] << '\t' << group << endl;
+ }else{ //you are a abund name
+ aout << names[i] << '\t' << group << endl;
+ }
+ }
+ }
+ }
+
+ rout.close();
+ aout.close();
+
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(groupfile));
+ ofstream* temp;
+ ofstream* temp2;
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+ for (int i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[Groups[i]+".rare"] = temp;
+ temp2 = new ofstream;
+ filehandles[Groups[i]+".abund"] = temp2;
+
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ variables["[group]"] = Groups[i];
+ m->openOutputFile(getOutputFileName("group",variables), *(filehandles[Groups[i]+".rare"]));
+ variables["[tag2]"] = "abund";
+ m->openOutputFile(getOutputFileName("group",variables), *(filehandles[Groups[i]+".abund"]));
+ }
+
+ for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
+ vector<string> 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
+ rareAbund = ".rare";
+ }else{ //you are a abund name
+ rareAbund = ".abund";
+ }
+
+ for (int i = 0; i < names.size(); i++) {
+
+ string group = groupMap.getGroup(names[i]);
+
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ *(filehandles[group+rareAbund]) << names[i] << '\t' << group << endl;
+ }
+ }
+ }
+
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(filehandles[it3->first])).close();
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = it3->first;
+ outputNames.push_back(getOutputFileName("group",variables)); outputTypes["group"].push_back(getOutputFileName("group",variables));
+ delete it3->second;
+ }
}
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "parseGroups");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::parseFasta(string tag) { //namefile
+ try {
+
+ map<string, ofstream*> filehandles;
+
+ if (Groups.size() == 0) {
+ ofstream aout;
+ ofstream rout;
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ string rare = getOutputFileName("fasta",variables);
+ m->openOutputFile(rare, rout);
+ outputNames.push_back(rare); outputTypes["fasta"].push_back(rare);
+
+ variables["[tag2]"] = "abund";
+ string abund = getOutputFileName("fasta",variables);
+ m->openOutputFile(abund, aout);
+ outputNames.push_back(abund); outputTypes["fasta"].push_back(abund);
+
+ //open input file
+ ifstream in;
+ m->openInputFile(fastafile, in);
- if (accnos) {
- outAccnosAbund.close(); outAccnosRare.close();
- if (!wroteAccnosRare) { remove((fileroot + "rare.accnos").c_str()); }
- else { outputNames.push_back((fileroot + "rare.accnos")); }
- if (!wroteAccnosAbund) { remove((fileroot + "abund.accnos").c_str()); }
- else { outputNames.push_back((fileroot + "abund.accnos")); }
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ Sequence seq(in); m->gobble(in);
+
+ if (seq.getName() != "") {
+
+ map<string, string>::iterator itNames;
+
+ itNames = nameMap.find(seq.getName());
+
+ if (itNames == nameMap.end()) {
+ m->mothurOut(seq.getName() + " is not in your names or list file, ignoring."); m->mothurOutEndLine();
+ }else{
+ if (rareNames.count(seq.getName()) != 0) { //you are a rare name
+ seq.printSequence(rout);
+ }else{ //you are a abund name
+ seq.printSequence(aout);
+ }
+ }
+ }
+ }
+ in.close();
+ rout.close();
+ aout.close();
+
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ ofstream* temp;
+ ofstream* temp2;
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+ for (int i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[Groups[i]+".rare"] = temp;
+ temp2 = new ofstream;
+ filehandles[Groups[i]+".abund"] = temp2;
+
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = "rare";
+ variables["[group]"] = Groups[i];
+ m->openOutputFile(getOutputFileName("fasta",variables), *(filehandles[Groups[i]+".rare"]));
+ variables["[tag2]"] = "abund";
+ m->openOutputFile(getOutputFileName("fasta",variables), *(filehandles[Groups[i]+".abund"]));
+ }
+
+ //open input file
+ ifstream in;
+ m->openInputFile(fastafile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ Sequence seq(in); m->gobble(in);
+
+ if (seq.getName() != "") {
+ map<string, string>::iterator itNames = nameMap.find(seq.getName());
+
+ if (itNames == nameMap.end()) {
+ m->mothurOut(seq.getName() + " is not in your names or list file, ignoring."); m->mothurOutEndLine();
+ }else{
+ vector<string> 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
+ rareAbund = ".rare";
+ }else{ //you are a abund name
+ rareAbund = ".abund";
+ }
+
+ if (countfile == "") {
+ for (int i = 0; i < names.size(); i++) {
+ string group = groupMap.getGroup(seq.getName());
+
+ if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ seq.printSequence(*(filehandles[group+rareAbund]));
+ }else if(group == "not found") {
+ m->mothurOut(seq.getName() + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
+ }
+ }
+ }else {
+ vector<string> thisSeqsGroups = ct.getGroups(names[0]); //we only need names[0], because there is no namefile
+ for (int i = 0; i < thisSeqsGroups.size(); i++) {
+ if (m->inUsersGroups(thisSeqsGroups[i], Groups)) { //only add if this is in a group we want
+ seq.printSequence(*(filehandles[thisSeqsGroups[i]+rareAbund]));
+ }
+ }
+ }
+ }
+ }
+ }
+ in.close();
+
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(filehandles[it3->first])).close();
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[tag]"] = tag;
+ variables["[tag2]"] = it3->first;
+ outputNames.push_back(getOutputFileName("fasta",variables)); outputTypes["fasta"].push_back(getOutputFileName("fasta",variables));
+ delete it3->second;
+ }
}
-
+
return 0;
}
catch(exception& e) {
- m->errorOut(e, "SplitAbundCommand", "split");
+ m->errorOut(e, "SplitAbundCommand", "parseFasta");
exit(1);
}
}
-
/**********************************************************************************************************************/
-
projects / mothur.git / blobdiff