SplitAbundCommand::SplitAbundCommand(string option) {
try {
abort = false;
- wroteRareList = false;
- wroteAbundList = false;
allLines = 1;
//allow user to run help
else {
//valid paramters for this command
- string Array[] = {"list","name","group","label","accnos","cutoff","outputdir","inputdir"};
+ string Array[] = {"name","group","label","accnos","groups","fasta","cutoff","outputdir","inputdir"}; //"list",
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
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);
+ //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()){
//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; }
- //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; }
+
+ 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; }
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();
if (error == 1) { abort = true; }
+
}
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else if (groups == "all") {
+ if (groupfile != "") { Groups = groupMap->namesOfGroups; }
+ else { m->mothurOut("You cannot select groups without a valid groupfile, I will disregard your groups selection. "); m->mothurOutEndLine(); groups = ""; }
+ }else {
+ 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 != "")) { m->mothurOut("You must either a listfile or a namefile for the split.abund command, but NOT BOTH. "); m->mothurOutEndLine(); abort = true; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
//**********************************************************************************************************************
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 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 list, name, cutoff, group, label, groups 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(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");
if (abort == true) { return 0; }
- if (namefile != "") { split(); }
- else {
+ if (listfile != "") { //you are using a listfile to determine abundance
//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 (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 the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
list = input->getListVector();
string lastLabel = list->getLabel();
+ //do you have a namefile or do we need to similate one?
+ 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; }
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 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());
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());
list = input->getListVector(lastLabel); //get new list vector to process
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
- split(list);
+ splitList(list);
delete list;
}
delete input;
+ for (map<string, bool>::iterator itBool = wroteListFile.begin(); itBool != wroteListFile.end(); itBool++) {
+ string filename = fileroot + itBool->first;
+ 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; }
+
+
+ }else { //you are using the namefile to determine abundance
+
+ 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); }
}
-
-
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
}
}
/**********************************************************************************************************************/
-int SplitAbundCommand::split(ListVector* thisList) {
+int SplitAbundCommand::splitList(ListVector* thisList) {
try {
-
- SAbundVector* sabund = new SAbundVector();
- *sabund = thisList->getSAbundVector();
+ rareNames.clear();
+ abundNames.clear();
- //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;
+ //get rareNames and abundNames
+ for (int i = 0; i < thisList->getNumBins(); i++) {
+ if (m->control_pressed) { return 0; }
+
+ string bin = thisList->get(i);
+
+ vector<string> names;
+ splitAtComma(bin, names); //parses bin into individual sequence names
+ int size = names.size();
+
+ if (size <= cutoff) {
+ 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
+
+ writeList(thisList);
+
+ string tag = thisList->getLabel() + ".";
+ if (groupfile != "") { parseGroup(tag); }
+ if (accnos) { writeAccnos(tag); }
+ if (fastafile != "") { parseFasta(tag); }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SplitAbundCommand", "splitList");
+ exit(1);
+ }
+}
+/**********************************************************************************************************************/
+int SplitAbundCommand::writeList(ListVector* thisList) {
+ try {
+
+ map<string, ofstream*> filehandles;
- //setup output files
- ofstream outListAbund;
- ofstream outListRare;
- ofstream outGroupRare;
- ofstream outGroupAbund;
- ofstream outAccnosRare;
- ofstream outAccnosAbund;
+ if (Groups.size() == 0) {
+ SAbundVector* sabund = new SAbundVector();
+ *sabund = thisList->getSAbundVector();
- 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';
+ //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;
+
+ 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';
+ }
- if (accnos) {
- string accnosName = fileroot + thisList->getLabel() + ".rare.accnos";
- openOutputFile(accnosName, outAccnosRare);
- outputNames.push_back(accnosName);
+ if (abundNames.size() != 0) {
+ string abund = outputDir + getRootName(getSimpleName(listfile)) + ".abund.list";
+ wroteListFile["abund"] = true;
+ openOutputFileAppend(abund, aout);
+ rout << thisList->getLabel() << '\t' << numAbundBins << '\t';
}
+
+ for (int i = 0; i < thisList->getNumBins(); i++) {
+ if (m->control_pressed) { break; }
+
+ string bin = list->get(i);
- if (groupfile != "") {
- string groupFileName = outputDir + getRootName(getSimpleName(groupfile)) + thisList->getLabel() + ".rare.group";
- openOutputFile(groupFileName, outGroupRare);
- outputNames.push_back(groupFileName);
+ int size = getNumNames(bin);
+
+ if (size <= cutoff) { rout << bin << '\t'; }
+ else { aout << bin << '\t'; }
}
- }
-
- if (numAbundBins > 0) {
- wroteAbundList = true;
- string listAbundName = fileroot + "abund.list";
- openOutputFileAppend(listAbundName, outListAbund);
- outListAbund << thisList->getLabel() << '\t' << numAbundBins << '\t';
- if (accnos) {
- string accnosName = fileroot + thisList->getLabel() + ".abund.accnos";
- openOutputFile(accnosName, outAccnosAbund);
- outputNames.push_back(accnosName);
+ if (rareNames.size() != 0) { rout << endl; rout.close(); }
+ if (abundNames.size() != 0) { aout << endl; aout.close(); }
+
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + getRootName(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;
+
+ openOutputFileAppend(fileroot + Groups[i] + ".rare.list", *(filehandles[Groups[i]+".rare"]));
+ openOutputFileAppend(fileroot + Groups[i] + ".abund.list", *(filehandles[Groups[i]+".abund"]));
}
- if (groupfile != "") {
- string groupFileName = outputDir + getRootName(getSimpleName(groupfile)) + thisList->getLabel() + ".abund.group";
- openOutputFile(groupFileName, outGroupAbund);
- outputNames.push_back(groupFileName);
+ 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; }
-
- string bin = list->get(i);
+ for (int i = 0; i < thisList->getNumBins(); i++) {
+ if (m->control_pressed) { break; }
- int size = getNumNames(bin);
+ map<string, string> groupBins;
+ string bin = list->get(i);
- if (size <= cutoff) { outListRare << bin << '\t'; }
- else { outListAbund << bin << '\t'; }
-
- if ((groupfile != "") || (accnos)) { //you need to parse the bin...
vector<string> names;
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; }
+ string rareAbund;
+ if (rareNames.count(names[j]) != 0) { //you are a rare name
+ rareAbund = ".rare";
+ }else{ //you are a abund name
+ rareAbund = ".abund";
}
- //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 group = groupMap->getGroup(names[j]);
+
+ if (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();
}
-
- }//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(); }
+ }
+
+
+ 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
+ wroteListFile[it3->first] = true;
+ (*(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::splitNames() { //namefile
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);
+ rareNames.clear();
+ abundNames.clear();
- if (accnos) {
- string accnosName = fileroot + "rare.accnos";
- openOutputFile(accnosName, outAccnosRare);
+ //open input file
+ ifstream in;
+ openInputFile(namefile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
- accnosName = fileroot + "abund.accnos";
- openOutputFile(accnosName, outAccnosAbund);
- }
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; gobble(in);
- if (groupfile != "") {
- string groupFileName = outputDir + getRootName(getSimpleName(groupfile)) + ".rare.group";
- openOutputFile(groupFileName, outGroupRare);
+ nameMap[firstCol] = secondCol;
- groupFileName = outputDir + getRootName(getSimpleName(groupfile)) + ".abund.group";
- openOutputFile(groupFileName, outGroupAbund);
+ int size = 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);
string firstCol, secondCol;
in >> firstCol >> secondCol; gobble(in);
- int size = getNumNames(secondCol);
+ nameMap[firstCol] = secondCol;
+ }
+ in.close();
+
+ 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;
+ splitAtComma(bin, names); //parses bin into individual sequence names
- if (size <= cutoff) { outNameRare << firstCol << '\t' << secondCol << endl; wroteNameRare = true; }
- else { outNameAbund << firstCol << '\t' << secondCol << endl; wroteNameAbund = true; }
+ 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::writeNames() { //namefile
+ try {
+
+ map<string, ofstream*> filehandles;
+
+ if (Groups.size() == 0) {
+ ofstream aout;
+ ofstream rout;
+
+ 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();
+ }
+
+ 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();
+ }
+
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + getRootName(getSimpleName(namefile));
+ 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;
+
+ 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;
+ }
- if ((groupfile != "") || (accnos)) { //you need to parse the bin...
+ for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {
vector<string> names;
- splitAtComma(secondCol, names); //parses bin into individual sequence names
+ 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]);
+
+ if (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;
+ wroteFile[itout->first] = true;
+ }
+ }
+
+
+ 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()); }
+ 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;
+
+ 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();
+ }
+
+ 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();
+ }
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + getRootName(getSimpleName(inputFile));
+ 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;
+
+ 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;
+ }
+
+ //write rare
+ for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
+ string group = groupMap->getGroup(*itRare);
- //write to groupfile
- if (groupfile != "") {
- string group = groupMap->getGroup(names[j]);
+ if (inUsersGroups(group, Groups)) { //only add if this is in a group we want
+ *(filehandles[group+".rare"]) << *itRare << endl;
+ wroteFile[group+".rare"] = true;
+ }
+ }
+
+ //write abund
+ for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
+ string group = groupMap->getGroup(*itAbund);
- 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 (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()); }
+ 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;
+
+ if (rareNames.size() != 0) {
+ string rare = outputDir + getRootName(getSimpleName(groupfile)) + tag + "rare.groups";
+ openOutputFile(rare, rout);
+ outputNames.push_back(rare);
+ }
+
+ 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
+
+ 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
+ rout << names[i] << '\t' << group << endl;
}
}
-
- }//end for names
- }//end if parse
- }//end while
+ }
+ }
+
+ if (rareNames.size() != 0) { rout.close(); }
+ if (abundNames.size() != 0) { aout.close(); }
+
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + getRootName(getSimpleName(groupfile));
+ 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;
+
+ 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;
+ }
+
+ 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
+
+ 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 (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()); }
+ 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;
- //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 (Groups.size() == 0) {
+ 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);
+ }
+
+
+ //open input file
+ ifstream in;
+ openInputFile(fastafile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
- 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")); }
- }
+ Sequence seq(in); 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 namesfile, 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();
+ if (rareNames.size() != 0) { rout.close(); }
+ if (abundNames.size() != 0) { aout.close(); }
+
+ }else{ //parse names by abundance and group
+ string fileroot = outputDir + getRootName(getSimpleName(fastafile));
+ 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;
+
+ 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;
+ }
+
+ //open input file
+ ifstream in;
+ 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); 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 namesfile, ignoring."); m->mothurOutEndLine();
+ }else{
+ vector<string> names;
+ 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";
+ }
+
+ for (int i = 0; i < names.size(); i++) {
+
+ string group = groupMap->getGroup(seq.getName());
+
+ if (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();
+ }
+ }
+ }
+ }
+ }
+ in.close();
+
+ 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()); }
+ delete it3->second;
+ }
}
-
+
return 0;
}
catch(exception& e) {
- m->errorOut(e, "SplitAbundCommand", "split");
+ m->errorOut(e, "SplitAbundCommand", "parseFasta");
exit(1);
}
}
-
/**********************************************************************************************************************/
-
projects / mothur.git / blobdiff