#include "binsequencecommand.h"
//**********************************************************************************************************************
-BinSeqCommand::BinSeqCommand(){
+BinSeqCommand::BinSeqCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- fastafile = globaldata->getFastaFile();
- namesfile = globaldata->getNameFile();
- openInputFile(fastafile, in);
+ abort = false;
+ allLines = 1;
+ labels.clear();
- fasta = new FastaMap();
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string AlignArray[] = {"fasta","label","name", "group","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += m->hasPath(globaldata->getListFile()); //if user entered a file with a path then preserve it
+ }
+
+
+ //make sure the user has already run the read.otu command
+ if (globaldata->getListFile() == "") {
+ m->mothurOut("You must read a listfile before running the bin.seqs command.");
+ m->mothurOutEndLine();
+ abort = true;
+ }
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("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 = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+ }
+
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the bin.seqs command."); m->mothurOutEndLine(); abort = true; }
+ else if (fastafile == "not open") { 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 = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //if the user has not specified any labels use the ones from read.otu
+ if (label == "") {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ }
+
+ namesfile = validParameter.validFile(parameters, "name", true);
+ if (namesfile == "not open") { abort = true; }
+ else if (namesfile == "not found") { namesfile = ""; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+
+ if (abort == false) {
+// m->openInputFile(fastafile, in);
+ fasta = new FastaMap();
+ if (groupfile != "") {
+ groupMap = new GroupMap(groupfile);
+
+ int error = groupMap->readMap();
+ if (error == 1) { delete groupMap; abort = true; }
+ }
+ }
+
+ }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function BinSeqCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BinSeqCommand class function BinSeqCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void BinSeqCommand::help(){
+ try {
+ m->mothurOut("The bin.seqs command can only be executed after a successful read.otu command of a listfile.\n");
+ m->mothurOut("The bin.seqs command parameters are fasta, name, label and group. The fasta parameter is required.\n");
+ m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n");
+ m->mothurOut("The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n");
+ m->mothurOut("Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, name=amazon.names).\n");
+ m->mothurOut("The default value for label is all lines in your inputfile.\n");
+ m->mothurOut("The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n");
+ m->mothurOut("If you provide a groupfile, then it also appends the sequences group to the name.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "help");
exit(1);
- }
+ }
}
//**********************************************************************************************************************
BinSeqCommand::~BinSeqCommand(){
- delete input;
- delete read;
- delete fasta;
- delete list;
+ //made new in execute
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ globaldata->gListVector = NULL;
+ delete fasta;
+ if (groupfile != "") { delete groupMap; globaldata->gGroupmap = NULL; }
+ }
}
//**********************************************************************************************************************
int BinSeqCommand::execute(){
try {
- int count = 1;
- string binnames, name, sequence;
+ if (abort == true) { return 0; }
+
+ int error = 0;
//read fastafile
- fasta->readFastaFile(in);
+ fasta->readFastaFile(fastafile);
+
//set format to list so input can get listvector
- globaldata->setFormat("list");
+// globaldata->setFormat("list");
//if user gave a namesfile then use it
if (namesfile != "") {
}
//read list file
- read = new ReadPhilFile(globaldata->getListFile());
+ read = new ReadOTUFile(globaldata->getListFile());
read->read(&*globaldata);
input = globaldata->ginput;
list = globaldata->gListVector;
+ string lastLabel = list->getLabel();
+
+ if (m->control_pressed) { return 0; }
+
+ //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;
+
- while(list != NULL){
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
- //make new folder for bin info
- //string foldername = "/" + getRootName(globaldata->getListFile()) + list->getLabel() + ".bins/";
- // mkdir(foldername.c_str());
+ error = process(list);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
- string outputFileName = getRootName(globaldata->getListFile()) + list->getLabel() + ".fasta";
- openOutputFile(outputFileName, out);
-
- cout << list->getLabel() << '\t' << count << endl;
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
- //for each bin in the list vector
- for (int i = 0; i < list->size(); i++) {
+ delete list;
+ list = input->getListVector(lastLabel);
- //create output file
- //string outputFileName = foldername + getRootName(globaldata->getListFile()) + "bin" + toString(i+1) + ".fasta";
- //openOutputFile(outputFileName, out);
-
- binnames = list->get(i);
- while (binnames.find_first_of(',') != -1) {
- name = binnames.substr(0,binnames.find_first_of(','));
- binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
-
- //do work for that name
- sequence = fasta->getSequence(name);
- if (sequence != "not found") {
- name = name + "|" + toString(i+1);
- out << ">" << name << endl;
- out << sequence << endl;
- }else {
- cout << name << " is missing from your fasta or name file. Please correct. " << endl;
- remove(outputFileName.c_str());
- return 0;
- }
-
- }
-
- //get last name
- sequence = fasta->getSequence(binnames);
- if (sequence != "not found") {
- name = binnames + "bin" + toString(i+1);
- out << ">" << name << endl;
- out << sequence << endl;
- }else {
- cout << binnames << " is missing from your fasta or name file. Please correct. " << endl;
- remove(outputFileName.c_str());
- return 0;
- }
- //out.close();
- }
- out.close();
+ error = process(list);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
}
+ lastLabel = list->getLabel();
+
+ delete list;
list = input->getListVector();
- count++;
}
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (list != NULL) { delete list; }
+ list = input->getListVector(lastLabel);
+
+ error = process(list);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ delete list;
+ }
+
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BinSeqCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BinSeqCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
void BinSeqCommand::readNamesFile() {
try {
vector<string> dupNames;
- openInputFile(namesfile, inNames);
+ m->openInputFile(namesfile, inNames);
string name, names, sequence;
dupNames.clear();
//parse names into vector
- splitAtComma(names, dupNames);
+ m->splitAtComma(names, dupNames);
//store names in fasta map
sequence = fasta->getSequence(name);
fasta->push_back(dupNames[i], sequence);
}
- gobble(inNames);
+ m->gobble(inNames);
}
inNames.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BinSeqCommand", "readNamesFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BinSeqCommand class function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
+//return 1 if error, 0 otherwise
+int BinSeqCommand::process(ListVector* list) {
+ try {
+ string binnames, name, sequence;
+
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->getListFile())) + list->getLabel() + ".fasta";
+ m->openOutputFile(outputFileName, out);
+
+ //save to output list of output file names
+ outputNames.push_back(outputFileName);
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ //for each bin in the list vector
+ for (int i = 0; i < list->size(); i++) {
+
+ if (m->control_pressed) { return 1; }
+
+ binnames = list->get(i);
+ while (binnames.find_first_of(',') != -1) {
+ name = binnames.substr(0,binnames.find_first_of(','));
+ binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
+
+ //do work for that name
+ sequence = fasta->getSequence(name);
+ if (sequence != "not found") {
+ //if you don't have groups
+ if (groupfile == "") {
+ name = name + "|" + toString(i+1);
+ out << ">" << name << endl;
+ out << sequence << endl;
+ }else {//if you do have groups
+ string group = groupMap->getGroup(name);
+ if (group == "not found") {
+ m->mothurOut(name + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
+ return 1;
+ }else{
+ name = name + "|" + group + "|" + toString(i+1);
+ out << ">" << name << endl;
+ out << sequence << endl;
+ }
+ }
+ }else {
+ m->mothurOut(name + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
+ return 1;
+ }
+
+ }
+
+ //get last name
+ sequence = fasta->getSequence(binnames);
+ if (sequence != "not found") {
+ //if you don't have groups
+ if (groupfile == "") {
+ binnames = binnames + "|" + toString(i+1);
+ out << ">" << binnames << endl;
+ out << sequence << endl;
+ }else {//if you do have groups
+ string group = groupMap->getGroup(binnames);
+ if (group == "not found") {
+ m->mothurOut(binnames + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
+ return 1;
+ }else{
+ binnames = binnames + "|" + group + "|" + toString(i+1);
+ out << ">" << binnames << endl;
+ out << sequence << endl;
+ }
+ }
+ }else {
+ m->mothurOut(binnames + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
+ return 1;
+ }
+ }
+
+ out.close();
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "process");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
projects / mothur.git / blobdiff