globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
//allow user to run help
else {
//valid paramters for this command
- string AlignArray[] = {"fasta","line","label","name", "group"};
+ string AlignArray[] = {"fasta","label","name", "group"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- parser = new OptionParser();
- parser->parse(option, parameters); delete parser;
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
- ValidParameters* validParameter = new ValidParameters();
+ ValidParameters validParameter;
//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; }
+ for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//make sure the user has already run the read.otu command
- if (globaldata->getListFile() == "") { cout << "You must read a listfile before running the bin.seqs command." << endl; abort = true; }
+ if (globaldata->getListFile() == "") {
+ mothurOut("You must read a listfile before running the bin.seqs command.");
+ mothurOutEndLine();
+ abort = true;
+ }
//check for required parameters
- fastafile = validParameter->validFile(parameters, "fasta", true);
- if (fastafile == "not found") { cout << "fasta is a required parameter for the bin.seqs command." << endl; abort = true; }
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not found") { mothurOut("fasta is a required parameter for the bin.seqs command."); mothurOutEndLine(); abort = true; }
else if (fastafile == "not open") { abort = true; }
- else {
- globaldata->setFastaFile(fastafile);
- openInputFile(fastafile, in);
- fasta = new FastaMap();
- }
-
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
- line = validParameter->validFile(parameters, "line", false);
- if (line == "not found") { line = ""; }
- else {
- if(line != "all") { splitAtDash(line, lines); allLines = 0; }
- else { allLines = 1; }
- }
- label = validParameter->validFile(parameters, "label", false);
+ label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
if(label != "all") { splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
- //if the user has not specified any line or labels use the ones from read.otu
- else if ((line == "") && (label == "")) {
+ //if the user has not specified any labels use the ones from read.otu
+ if (label == "") {
allLines = globaldata->allLines;
labels = globaldata->labels;
- lines = globaldata->lines;
}
- namesfile = validParameter->validFile(parameters, "name", true);
+ namesfile = validParameter.validFile(parameters, "name", true);
if (namesfile == "not open") { abort = true; }
else if (namesfile == "not found") { namesfile = ""; }
- groupfile = validParameter->validFile(parameters, "group", true);
+ groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
- else {
- //read in group map info.
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+
+ if (abort == false) {
+// openInputFile(fastafile, in);
+ fasta = new FastaMap();
+ if (groupfile != "") {
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+ }
}
- delete validParameter;
}
}
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";
+ 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";
- exit(1);
- }
}
//**********************************************************************************************************************
void BinSeqCommand::help(){
try {
- cout << "The bin.seqs command can only be executed after a successful read.otu command of a listfile." << "\n";
- cout << "The bin.seqs command parameters are fasta, name, line, label and group. The fasta parameter is required, and you may not use line and label at the same time." << "\n";
- cout << "The line and label allow you to select what distance levels you would like a output files created for, and are separated by dashes." << "\n";
- cout << "The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, line=yourLines, label=yourLabels)." << "\n";
- cout << "Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, line=1-3-5, name=amazon.names)." << "\n";
- cout << "The default value for line and label are all lines in your inputfile." << "\n";
- cout << "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name." << "\n";
- cout << "If you provide a groupfile, then it also appends the sequences group to the name." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
+ mothurOut("The bin.seqs command can only be executed after a successful read.otu command of a listfile.\n");
+ mothurOut("The bin.seqs command parameters are fasta, name, label and group. The fasta parameter is required.\n");
+ 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");
+ mothurOut("The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n");
+ mothurOut("Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, name=amazon.names).\n");
+ mothurOut("The default value for label is all lines in your inputfile.\n");
+ mothurOut("The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n");
+ mothurOut("If you provide a groupfile, then it also appends the sequences group to the name.\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BinSeqCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "BinSeqCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BinSeqCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
-
-
//**********************************************************************************************************************
BinSeqCommand::~BinSeqCommand(){
//made new in execute
if (abort == false) {
- delete input;
+ delete input; globaldata->ginput = NULL;
delete read;
- delete list;
+ globaldata->gListVector = NULL;
+ delete fasta;
+ if (groupfile != "") { delete groupMap; globaldata->gGroupmap = NULL; }
}
-
- //made new in constructor
- delete fasta;
- if (groupfile != "") {
- delete groupMap;
- }
-
}
//**********************************************************************************************************************
int BinSeqCommand::execute(){
try {
-
if (abort == true) { return 0; }
- int count = 1;
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 != "") {
input = globaldata->ginput;
list = globaldata->gListVector;
- ListVector* lastList = list;
+ string lastLabel = list->getLabel();
//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;
- set<int> userLines = lines;
- while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
- error = process(list, count);
+ error = process(list);
if (error == 1) { return 0; }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
+ if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete list;
+ list = input->getListVector(lastLabel);
- error = process(lastList, count);
+ error = process(list);
if (error == 1) { return 0; }
- processedLabels.insert(lastList->getLabel());
- userLabels.erase(lastList->getLabel());
-
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
}
- if (count != 1) { delete lastList; }
- lastList = list;
-
+ lastLabel = list->getLabel();
+
+ delete list;
list = input->getListVector();
- count++;
}
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastList->getLabel()) != 1) {
- cout << ". I will use " << lastList->getLabel() << "." << endl;
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- error = process(lastList, count);
- if (error == 1) { return 0; }
+ if (list != NULL) { delete list; }
+ list = input->getListVector(lastLabel);
+
+ error = process(list);
+ if (error == 1) { return 0; }
+
+ delete list;
}
- delete lastList;
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";
+ 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);
- }
}
//**********************************************************************************************************************
}
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";
+ 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, int count) {
+int BinSeqCommand::process(ListVector* list) {
try {
string binnames, name, sequence;
string outputFileName = getRootName(globaldata->getListFile()) + list->getLabel() + ".fasta";
openOutputFile(outputFileName, out);
- cout << list->getLabel() << '\t' << count << endl;
+ mothurOut(list->getLabel()); mothurOutEndLine();
//for each bin in the list vector
for (int i = 0; i < list->size(); i++) {
}else {//if you do have groups
string group = groupMap->getGroup(name);
if (group == "not found") {
- cout << name << " is missing from your group file. Please correct. " << endl;
+ mothurOut(name + " is missing from your group file. Please correct. "); mothurOutEndLine();
remove(outputFileName.c_str());
return 1;
}else{
}
}
}else {
- cout << name << " is missing from your fasta or name file. Please correct. " << endl;
+ mothurOut(name + " is missing from your fasta or name file. Please correct. "); mothurOutEndLine();
remove(outputFileName.c_str());
return 1;
}
}else {//if you do have groups
string group = groupMap->getGroup(binnames);
if (group == "not found") {
- cout << binnames << " is missing from your group file. Please correct. " << endl;
+ mothurOut(binnames + " is missing from your group file. Please correct. "); mothurOutEndLine();
remove(outputFileName.c_str());
return 1;
}else{
}
}
}else {
- cout << binnames << " is missing from your fasta or name file. Please correct. " << endl;
+ mothurOut(binnames + " is missing from your fasta or name file. Please correct. "); mothurOutEndLine();
remove(outputFileName.c_str());
return 1;
}
}
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";
+ errorOut(e, "BinSeqCommand", "process");
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);
- }
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff