#include "binsequencecommand.h"
//**********************************************************************************************************************
-BinSeqCommand::BinSeqCommand(string option){
+BinSeqCommand::BinSeqCommand(string option) {
try {
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 += 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() == "") {
- mothurOut("You must read a listfile before running the bin.seqs command.");
- mothurOutEndLine();
+ 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") { mothurOut("fasta is a required parameter for the bin.seqs command."); mothurOutEndLine(); abort = 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...
- 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 {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
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);
else if (groupfile == "not found") { groupfile = ""; }
if (abort == false) {
-// openInputFile(fastafile, in);
+// m->openInputFile(fastafile, in);
fasta = new FastaMap();
if (groupfile != "") {
groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+
+ int error = groupMap->readMap();
+ if (error == 1) { delete groupMap; abort = true; }
}
}
}
}
catch(exception& e) {
- errorOut(e, "BinSeqCommand", "BinSeqCommand");
+ m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
exit(1);
}
}
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 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");
+ 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) {
- errorOut(e, "BinSeqCommand", "help");
+ m->errorOut(e, "BinSeqCommand", "help");
exit(1);
}
}
try {
if (abort == true) { return 0; }
- int count = 1;
int error = 0;
//read fastafile
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;
- set<int> userLines = lines;
- while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ 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(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
- error = process(list, count);
- if (error == 1) { return 0; }
+ 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());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
delete list;
list = input->getListVector(lastLabel);
- error = process(list, count);
- if (error == 1) { return 0; }
+ 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++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- delete list;
+ if (list != NULL) { delete list; }
list = input->getListVector(lastLabel);
- error = process(list, count);
- if (error == 1) { return 0; }
+ 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) {
- errorOut(e, "BinSeqCommand", "execute");
+ m->errorOut(e, "BinSeqCommand", "execute");
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) {
- errorOut(e, "BinSeqCommand", "readNamesFile");
+ m->errorOut(e, "BinSeqCommand", "readNamesFile");
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);
+
+ 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);
- mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ 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(','));
}else {//if you do have groups
string group = groupMap->getGroup(name);
if (group == "not found") {
- mothurOut(name + " is missing from your group file. Please correct. "); mothurOutEndLine();
- remove(outputFileName.c_str());
+ m->mothurOut(name + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
return 1;
}else{
name = name + "|" + group + "|" + toString(i+1);
}
}
}else {
- mothurOut(name + " is missing from your fasta or name file. Please correct. "); mothurOutEndLine();
- remove(outputFileName.c_str());
+ m->mothurOut(name + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
return 1;
}
}else {//if you do have groups
string group = groupMap->getGroup(binnames);
if (group == "not found") {
- mothurOut(binnames + " is missing from your group file. Please correct. "); mothurOutEndLine();
- remove(outputFileName.c_str());
+ m->mothurOut(binnames + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
return 1;
}else{
binnames = binnames + "|" + group + "|" + toString(i+1);
}
}
}else {
- mothurOut(binnames + " is missing from your fasta or name file. Please correct. "); mothurOutEndLine();
- remove(outputFileName.c_str());
+ m->mothurOut(binnames + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
return 1;
}
}
}
catch(exception& e) {
- errorOut(e, "BinSeqCommand", "process");
+ m->errorOut(e, "BinSeqCommand", "process");
exit(1);
}
}
projects / mothur.git / blobdiff