#include "binsequencecommand.h"
+
//**********************************************************************************************************************
-vector<string> BinSeqCommand::getValidParameters(){
- try {
- string AlignArray[] = {"fasta","label","name", "group","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "BinSeqCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> BinSeqCommand::getRequiredParameters(){
+vector<string> BinSeqCommand::setParameters(){
try {
- string AlignArray[] = {"fasta"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "BinSeqCommand", "getRequiredParameters");
+ m->errorOut(e, "BinSeqCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> BinSeqCommand::getRequiredFiles(){
+string BinSeqCommand::getHelpString(){
try {
- string AlignArray[] = {"list"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- return myArray;
+ string helpString = "";
+ helpString += "The bin.seqs command parameters are list, fasta, name, label and group. The fasta and list are required, unless you have a valid current list and fasta file.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n";
+ helpString += "The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n";
+ helpString += "Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, name=amazon.names).\n";
+ helpString += "The default value for label is all lines in your inputfile.\n";
+ helpString += "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n";
+ helpString += "If you provide a groupfile, then it also appends the sequences group to the name.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "BinSeqCommand", "getRequiredFiles");
+ m->errorOut(e, "BinSeqCommand", "getHelpString");
exit(1);
}
}
BinSeqCommand::BinSeqCommand(){
try {
abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
}
//**********************************************************************************************************************
BinSeqCommand::BinSeqCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
abort = false; calledHelp = false;
allLines = 1;
labels.clear();
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string AlignArray[] = {"fasta","label","name", "group","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
- //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 = ""; }
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
+ it = parameters.find("list");
+ //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["list"] = inputDir + it->second; }
+ }
+
it = parameters.find("name");
//user has given a template file
if(it != parameters.end()){
//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; }
+ if (fastafile == "not found") { //if there is a current phylip file, use it
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
else if (fastafile == "not open") { abort = true; }
+
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not found") {
+ listfile = m->getListFile();
+ if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+ else if (listfile == "not open") { listfile = ""; 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(listfile); //if user entered a file with a path then preserve it
+ }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
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 = ""; }
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) {
}
//**********************************************************************************************************************
-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(){
- //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; }
- }
-}
-
+BinSeqCommand::~BinSeqCommand(){}
//**********************************************************************************************************************
int BinSeqCommand::execute(){
int error = 0;
+ fasta = new FastaMap();
+ if (groupfile != "") {
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+ }
+
//read fastafile
fasta->readFastaFile(fastafile);
-
- //set format to list so input can get listvector
-// globaldata->setFormat("list");
-
//if user gave a namesfile then use it
if (namesfile != "") {
readNamesFile();
}
- //read list file
- read = new ReadOTUFile(globaldata->getListFile());
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- list = globaldata->gListVector;
+ input = new InputData(listfile, "list");
+ list = input->getListVector();
string lastLabel = list->getLabel();
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { delete input; delete fasta; if (groupfile != "") { delete groupMap; } 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;
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(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
if(allLines == 1 || labels.count(list->getLabel()) == 1){
error = process(list);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
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; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
list = input->getListVector();
}
- if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
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; }
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
delete list;
}
- if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
-
+ delete input;
+ delete fasta;
+ if (groupfile != "") { delete groupMap; }
+
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ delete input;
+ delete fasta;
+ if (groupfile != "") { delete groupMap; }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
try {
string binnames, name, sequence;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->getListFile())) + list->getLabel() + ".fasta";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".fasta";
m->openOutputFile(outputFileName, out);
//save to output list of output file names
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