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","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 (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ 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 += 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() == "") {
mothurOut("You must read a listfile before running the bin.seqs command.");
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 = 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 = 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 = 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);
//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);
if (label == "not found") { label = ""; }
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); 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);
fasta = new FastaMap();
if (groupfile != "") {
groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+
+ int error = groupMap->readMap();
+ if (error == 1) { delete groupMap; abort = true; }
}
}
void BinSeqCommand::help(){
try {
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, line, label and group. The fasta parameter is required, and you may not use line and label at the same time.\n");
- mothurOut("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");
- mothurOut("The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, line=yourLines, label=yourLabels).\n");
- mothurOut("Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, line=1-3-5, name=amazon.names).\n");
- mothurOut("The default value for line and label are all lines in your inputfile.\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");
try {
if (abort == true) { return 0; }
- int count = 1;
int error = 0;
//read fastafile
//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);
if (error == 1) { return 0; }
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
- userLines.erase(count);
}
if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
delete list;
list = input->getListVector(lastLabel);
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++;
}
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
if (list != NULL) { delete list; }
list = input->getListVector(lastLabel);
int BinSeqCommand::process(ListVector* list) {
try {
string binnames, name, sequence;
- string outputFileName = getRootName(globaldata->getListFile()) + list->getLabel() + ".fasta";
+
+ string outputFileName = outputDir + getRootName(getSimpleName(globaldata->getListFile())) + list->getLabel() + ".fasta";
openOutputFile(outputFileName, out);
mothurOut(list->getLabel()); mothurOutEndLine();
projects / mothur.git / blobdiff