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|
/*
* splitabundcommand.cpp
* Mothur
*
* Created by westcott on 5/17/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "splitabundcommand.h"
#include "getseqscommand.h"
#include "getotuscommand.h"
//**********************************************************************************************************************
vector<string> SplitAbundCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,false,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "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 pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["count"] = tempOutNames;
abort = false; calledHelp = false; allLines = true;
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 or a list or a names or a count file splits the sequences into rare and abundant groups. \n";
helpString += "The split.abund command parameters are fasta, list, name, count, cutoff, group, label and cutoff.\n";
helpString += "The fasta or 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. If cutoff < 1, mothur assumes this is a percentage. 0.02 -> rare reads represent <= 2% of total reads. \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 += "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";
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"; }
else if (type == "list") { pattern = "[filename],[tag],[tag2],list"; }
else if (type == "name") { pattern = "[filename],[tag],names-[filename],[tag],[tag2],names"; }
else if (type == "count") { pattern = "[filename],[tag],[tag2],count_table-[filename],[tag],count_table"; }
else if (type == "group") { pattern = "[filename],[tag],[tag2],groups"; }
else if (type == "accnos") { pattern = "[filename],[tag],[tag2],accnos"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "SplitAbundCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
SplitAbundCommand::SplitAbundCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
//check for required parameters
listfile = validParameter.validFile(parameters, "list");
if (listfile == "not open") { abort = true; }
else if (listfile == "not found") { listfile = ""; }
else{ inputFile = listfile; current->setListFile(listfile); }
namefile = validParameter.validFile(parameters, "name");
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
else{ inputFile = namefile; current->setNameFile(namefile); }
fastafile = validParameter.validFile(parameters, "fasta");
if (fastafile == "not open") { abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
else { current->setFastaFile(fastafile); }
groupfile = validParameter.validFile(parameters, "group");
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else { current->setGroupFile(groupfile); }
countfile = validParameter.validFile(parameters, "count");
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else {
current->setCountFile(countfile);
ct.readTable(countfile, true, false);
}
if ((namefile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: name or count.\n"); abort = true;
}
if ((groupfile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: group or count.\n"); abort=true;
}
//do you have all files needed
if ((listfile == "") && (namefile == "") && (countfile == "") && (fastafile == "")) {
namefile = current->getNameFile();
if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter.\n"); }
else {
listfile = current->getListFile();
if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter.\n"); }
else {
countfile = current->getCountFile();
if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter.\n"); }
else {
fastafile = current->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter.\n"); }
else { m->mothurOut("You have no current fastafile file, and a fasta, list, name or count file is required.\n"); abort = true; } }
}
}
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.valid(parameters, "label");
if (label == "not found") { label = ""; allLines = true; }
else {
if(label != "all") { util.splitAtDash(label, labels); allLines = false; }
else { allLines = true; }
}
string temp = validParameter.valid(parameters, "accnos"); if (temp == "not found") { temp = "F"; }
accnos = util.isTrue(temp);
temp = validParameter.valid(parameters, "cutoff"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, cutoff);
if (cutoff == 0) { m->mothurOut("[ERROR]: You must provide a cutoff to qualify what is abundant for the split.abund command. \n"); abort = true; }
}
}
catch(exception& e) {
m->errorOut(e, "SplitAbundCommand", "SplitAbundCommand");
exit(1);
}
}
//**********************************************************************************************************************
SplitAbundCommand::~SplitAbundCommand(){}
//**********************************************************************************************************************
int SplitAbundCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
if (listfile != "") { splitList(); }
else if (namefile != "") { splitNames(); }
else if (countfile != "") { splitCount(); }
//set fasta file as new current fastafile
string currentName = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setFastaFile(currentName); }
}
itTypes = outputTypes.find("name");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setNameFile(currentName); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setGroupFile(currentName); }
}
itTypes = outputTypes.find("list");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setListFile(currentName); }
}
itTypes = outputTypes.find("accnos");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setAccnosFile(currentName); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setCountFile(currentName); }
}
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "SplitAbundCommand", "execute");
exit(1);
}
}
/**********************************************************************************************************************/
int SplitAbundCommand::splitList() {
try {
InputData input(listfile, "list", nullVector);
set<string> processedLabels;
set<string> userLabels = labels;
string lastLabel = "";
ListVector* list = util.getNextList(input, allLines, userLabels, processedLabels, lastLabel);
if (cutoff < 1) { //percentage instead of raw count
int total = list->getNumSeqs();
if (countfile != "") { total = ct.getNumSeqs(); }
else if (namefile != "") { total = util.scanNames(namefile); }
float percentage = cutoff;
cutoff = int(percentage * total);
m->mothurOut("\nSetting cutoff to " + toString(cutoff) + "\n");
}
if (m->getControl_pressed()) { delete list; return 0; }
while (list != nullptr) {
if (m->getControl_pressed()) { delete list; break; }
process(list); delete list;
list = util.getNextList(input, allLines, userLabels, processedLabels, lastLabel);
}
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
return 0;
}
catch(exception& e) {
m->errorOut(e, "SplitAbundCommand", "splitList");
exit(1);
}
}
/**********************************************************************************************************************/
int SplitAbundCommand::process(ListVector* thisList) {
try {
set<string> rareNames;
set<string> abundNames;
set<string> abundOTUs, rareOTUs;
//get rareNames and abundNames
for (int i = 0; i < thisList->getNumBins(); i++) {
if (m->getControl_pressed()) { return 0; }
string bin = thisList->get(i);
vector<string> names;
util.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) {
for (int j = 0; j < names.size(); j++) { rareNames.insert(names[j]); }
rareOTUs.insert(thisList->getOTUName(i));
}else{
for (int j = 0; j < names.size(); j++) { abundNames.insert(names[j]); }
abundOTUs.insert(thisList->getOTUName(i));
}
}//end for
string tag = thisList->getLabel();
vector<string> accnosOTUs = writeAccnos(tag+"_OTUS", rareOTUs, abundOTUs); //return rare, abund accnos files
map<string, string> variables;
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir = util.hasPath(listfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(listfile));
variables["[tag]"] = tag;
variables["[tag2]"] = "rare";
string rareList = getOutputFileName("list",variables);
variables["[tag2]"] = "abund";
string abundList = getOutputFileName("list",variables);
string inputString = "accnos=" + accnosOTUs[0] + ", list=" + listfile + ", label=" + tag; //get rare
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: get.otus(" + inputString + ")\n");
Command* getOTUSCommand = new GetOtusCommand(inputString);
getOTUSCommand->execute();
map<string, vector<string> > filenames = getOTUSCommand->getOutputFiles();
delete getOTUSCommand;
util.renameFile(filenames["list"][0], rareList);
outputNames.push_back(rareList); outputTypes["list"].push_back(rareList);
m->mothurOut("/******************************************/\nDone.\n");
inputString = "accnos=" + accnosOTUs[1] + ", list=" + listfile+ ", label=" + tag;
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: get.otus(" + inputString + ")\n");
getOTUSCommand = new GetOtusCommand(inputString);
getOTUSCommand->execute();
filenames = getOTUSCommand->getOutputFiles();
delete getOTUSCommand;
util.renameFile(filenames["list"][0], abundList);
outputNames.push_back(abundList); outputTypes["list"].push_back(abundList);
m->mothurOut("/******************************************/\nDone.\n");
string rareCount, abundCount, rareName, abundName, rareFasta, abundFasta, rareGroup, abundGroup;
string inputString2 = "";
if (countfile != "") {
if (outputdir == "") { thisOutputDir = util.hasPath(countfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(countfile));
variables["[tag]"] = tag;
variables["[tag2]"] = "rare";
rareCount = getOutputFileName("count",variables);
variables["[tag2]"] = "abund";
abundCount = getOutputFileName("count",variables);
inputString2 += ", count=" + countfile;
}else if (groupfile != "") {
if (outputdir == "") { thisOutputDir = util.hasPath(groupfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(groupfile));
variables["[tag]"] = tag;
variables["[tag2]"] = "rare";
rareGroup = getOutputFileName("group",variables);
variables["[tag2]"] = "abund";
abundGroup = getOutputFileName("group",variables);
inputString2 += ", group=" + groupfile;
}
if (fastafile != "") {
if (outputdir == "") { thisOutputDir = util.hasPath(fastafile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(fastafile));
variables["[tag]"] = tag;
variables["[tag2]"] = "rare";
rareFasta = getOutputFileName("fasta",variables);
variables["[tag2]"] = "abund";
abundFasta = getOutputFileName("fasta",variables);
inputString2 += ", fasta=" + fastafile;
}
if (namefile != "") {
if (outputdir == "") { thisOutputDir = util.hasPath(namefile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(namefile));
variables["[tag]"] = tag;
variables["[tag2]"] = "rare";
rareName = getOutputFileName("name",variables);
variables["[tag2]"] = "abund";
abundName = getOutputFileName("name",variables);
inputString2 += ", name=" + namefile;
}
if (inputString2 != "") {
vector<string> accnosNames = writeAccnos(tag, rareNames, abundNames); //return rare, abund accnos files
inputString = "dups=t, accnos=" + accnosNames[0]; //get rare
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: get.seqs(" + inputString + inputString2 + ")\n");
Command* getCommand = new GetSeqsCommand(inputString+ inputString2);
getCommand->execute();
map<string, vector<string> > filenames = getCommand->getOutputFiles();
delete getCommand;
if (countfile != "") {
util.renameFile(filenames["count"][0], rareCount);
outputNames.push_back(rareCount); outputTypes["count"].push_back(rareCount);
}
else if (groupfile != "") {
util.renameFile(filenames["group"][0], rareGroup);
outputNames.push_back(rareGroup); outputTypes["group"].push_back(rareGroup);
}
if (fastafile != "") {
util.renameFile(filenames["fasta"][0], rareFasta);
outputNames.push_back(rareFasta); outputTypes["fasta"].push_back(rareFasta);
}
if (namefile != "") {
util.renameFile(filenames["name"][0], rareName);
outputNames.push_back(rareName); outputTypes["name"].push_back(rareName);
}
m->mothurOut("/******************************************/\nDone.\n");
inputString = "dups=t, accnos=" + accnosNames[1]; //get rare
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: get.seqs(" + inputString + inputString2 + ")\n");
getCommand = new GetSeqsCommand(inputString+ inputString2);
getCommand->execute();
filenames = getCommand->getOutputFiles();
delete getCommand;
if (countfile != "") { util.renameFile(filenames["count"][0], abundCount); outputNames.push_back(abundCount); outputTypes["count"].push_back(abundCount); }
else if (groupfile != "") { util.renameFile(filenames["group"][0], abundGroup);
outputNames.push_back(abundGroup); outputTypes["group"].push_back(abundGroup);
}
if (fastafile != "") { util.renameFile(filenames["fasta"][0], abundFasta); outputNames.push_back(abundFasta); outputTypes["fasta"].push_back(abundFasta); }
if (namefile != "") { util.renameFile(filenames["name"][0], abundName); outputNames.push_back(abundName); outputTypes["name"].push_back(abundName); }
m->mothurOut("/******************************************/\nDone.\n");
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "SplitAbundCommand", "process");
exit(1);
}
}
/**********************************************************************************************************************/
int SplitAbundCommand::splitCount() { //countfile
try {
inputFile = countfile;
set<string> rareNames;
set<string> abundNames;
if (cutoff < 1) { //cutoff is a percentage rather than a explicit size
float percentage = cutoff;
int totalSeqs = ct.getNumSeqs();
cutoff = int(totalSeqs * percentage);
m->mothurOut("\nSetting cutoff to " + toString(cutoff) + "\n");
}
vector<string> allNames = ct.getNamesOfSeqs();
for (int i = 0; i < allNames.size(); i++) {
if (m->getControl_pressed()) { return 0; }
int size = ct.getNumSeqs(allNames[i]);
if (size <= cutoff) {
rareNames.insert(allNames[i]);
}else{
abundNames.insert(allNames[i]);
}
}
vector<string> accnosNames = writeAccnos("", rareNames, abundNames); //return rare, abund accnos files
map<string, string> variables;
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir = util.hasPath(fastafile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(fastafile));
variables["[tag]"] = "";
variables["[tag2]"] = "rare";
string rareFasta = getOutputFileName("fasta",variables);
variables["[tag2]"] = "abund";
string abundFasta = getOutputFileName("fasta",variables);
if (outputdir == "") { thisOutputDir = util.hasPath(countfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(countfile));
variables["[tag]"] = "";
variables["[tag2]"] = "rare";
string rareCount = getOutputFileName("count",variables);
variables["[tag2]"] = "abund";
string abundCount = getOutputFileName("count",variables);
string inputString = "dups=t, accnos=" + accnosNames[0] + ", count=" + countfile; //get rare
if (fastafile != "") { inputString += ", fasta=" + fastafile; }
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: get.seqs(" + inputString + ")\n");
Command* getCommand = new GetSeqsCommand(inputString);
getCommand->execute();
map<string, vector<string> > filenames = getCommand->getOutputFiles();
delete getCommand;
util.renameFile(filenames["count"][0], rareCount);
outputNames.push_back(rareCount); outputTypes["count"].push_back(rareCount);
if (fastafile != "") { util.renameFile(filenames["fasta"][0], rareFasta); outputNames.push_back(rareFasta); outputTypes["fasta"].push_back(rareFasta); }
m->mothurOut("/******************************************/\nDone.\n");
inputString = "dups=t, accnos=" + accnosNames[1] + ", count=" + countfile; //get rare
if (fastafile != "") { inputString += ", fasta=" + fastafile; }
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: get.seqs(" + inputString + ")\n");
getCommand = new GetSeqsCommand(inputString);
getCommand->execute();
filenames = getCommand->getOutputFiles();
delete getCommand;
util.renameFile(filenames["count"][0], abundCount);
outputNames.push_back(abundCount); outputTypes["count"].push_back(abundCount);
if (fastafile != "") { util.renameFile(filenames["fasta"][0], abundFasta); outputNames.push_back(abundFasta); outputTypes["fasta"].push_back(abundFasta); }
m->mothurOut("/******************************************/\nDone.\n");
return 0;
}
catch(exception& e) {
m->errorOut(e, "SplitAbundCommand", "splitCount");
exit(1);
}
}
/**********************************************************************************************************************/
int SplitAbundCommand::splitNames() { //namefile
try {
set<string> rareNames;
set<string> abundNames;
if (cutoff < 1) { //percentage used, find cutoff value
float percentage = cutoff;
int totalSeqs = util.scanNames(namefile);
cutoff = int(totalSeqs * percentage);
m->mothurOut("\nSetting cutoff to " + toString(cutoff) + "\n");
}
//open input file
ifstream in; util.openInputFile(namefile, in);
while (!in.eof()) {
if (m->getControl_pressed()) { break; }
string firstCol, secondCol;
in >> firstCol; gobble(in); in >> secondCol; gobble(in);
int size = util.getNumNames(secondCol);
if (size <= cutoff) {
rareNames.insert(firstCol);
}else{
abundNames.insert(firstCol);
}
}
in.close();
vector<string> accnosNames = writeAccnos("", rareNames, abundNames); //return rare, abund accnos files
map<string, string> variables;
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir = util.hasPath(groupfile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(groupfile));
variables["[tag]"] = "";
variables["[tag2]"] = "rare";
string rareGroup = getOutputFileName("group",variables);
variables["[tag2]"] = "abund";
string abundGroup = getOutputFileName("group",variables);
if (outputdir == "") { thisOutputDir = util.hasPath(fastafile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(fastafile));
variables["[tag]"] = "";
variables["[tag2]"] = "rare";
string rareFasta = getOutputFileName("fasta",variables);
variables["[tag2]"] = "abund";
string abundFasta = getOutputFileName("fasta",variables);
if (outputdir == "") { thisOutputDir = util.hasPath(namefile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(namefile));
variables["[tag]"] = "";
variables["[tag2]"] = "rare";
string rareName = getOutputFileName("name",variables);
variables["[tag2]"] = "abund";
string abundName = getOutputFileName("name",variables);
string inputString = "dups=t, accnos=" + accnosNames[0] + ", name=" + namefile; //get rare
if (groupfile != "") { inputString += ", group=" + groupfile; }
if (fastafile != "") { inputString += ", fasta=" + fastafile; }
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: get.seqs(" + inputString + ")\n");
Command* getCommand = new GetSeqsCommand(inputString);
getCommand->execute();
map<string, vector<string> > filenames = getCommand->getOutputFiles();
delete getCommand;
util.renameFile(filenames["name"][0], rareName);
outputNames.push_back(rareName); outputTypes["name"].push_back(rareName);
if (groupfile != "") { util.renameFile(filenames["group"][0], rareGroup); outputNames.push_back(rareGroup); outputTypes["group"].push_back(rareGroup); }
if (fastafile != "") { util.renameFile(filenames["fasta"][0], rareFasta); outputNames.push_back(rareFasta); outputTypes["fasta"].push_back(rareFasta); }
m->mothurOut("/******************************************/\nDone.\n");
inputString = "dups=t, accnos=" + accnosNames[1] + ", name=" + namefile; //get rare
if (groupfile != "") { inputString += ", group=" + groupfile; }
if (fastafile != "") { inputString += ", fasta=" + fastafile; }
m->mothurOut("/******************************************/\n");
m->mothurOut("Running command: get.seqs(" + inputString + ")\n");
getCommand = new GetSeqsCommand(inputString);
getCommand->execute();
filenames = getCommand->getOutputFiles();
delete getCommand;
util.renameFile(filenames["name"][0], abundName);
outputNames.push_back(abundName); outputTypes["name"].push_back(abundName);
if (groupfile != "") { util.renameFile(filenames["group"][0], abundGroup); outputNames.push_back(abundGroup); outputTypes["group"].push_back(abundGroup); }
if (fastafile != "") { util.renameFile(filenames["fasta"][0], abundFasta); outputNames.push_back(abundFasta); outputTypes["fasta"].push_back(abundFasta); }
m->mothurOut("/******************************************/\nDone.\n");
return 0;
}
catch(exception& e) {
m->errorOut(e, "SplitAbundCommand", "splitNames");
exit(1);
}
}
/**********************************************************************************************************************/
//just write the unique names - if a namesfile is given
vector<string> SplitAbundCommand::writeAccnos(string tag, set<string> rareNames, set<string> abundNames) {
try {
vector<string> outputAccnosFiles;
map<string, string> variables;
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir = util.hasPath(inputFile); }
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(inputFile));
variables["[tag]"] = tag;
variables["[tag2]"] = "rare";
string rare = getOutputFileName("accnos",variables);
outputAccnosFiles.push_back(rare);
ofstream aout, rout;
util.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);
util.openOutputFile(abund, aout);
outputNames.push_back(abund); outputTypes["accnos"].push_back(abund);
outputAccnosFiles.push_back(abund);
for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) { aout << (*itAbund) << endl; }
aout.close();
return outputAccnosFiles;
}
catch(exception& e) {
m->errorOut(e, "SplitAbundCommand", "writeAccnos");
exit(1);
}
}
/**********************************************************************************************************************/
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