#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;
+ lines.clear();
+ 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","line","label","name", "group"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ 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; }
+
+
+ //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; }
+ else if (fastafile == "not open") { abort = true; }
+ else {
+ 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);
+ 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 == "")) {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ lines = globaldata->lines;
+ }
+
+ 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 = ""; }
+ else {
+ //read in group map info.
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+ }
+
+ }
}
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";
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";
+ }
+ 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";
+ 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(){
- delete input;
- delete read;
+ //made new in execute
+ if (abort == false) {
+ delete input;
+ delete read;
+ delete list;
+ }
+
+ //made new in constructor
delete fasta;
- delete list;
+ if (groupfile != "") {
+ delete groupMap;
+ }
+
}
//**********************************************************************************************************************
int BinSeqCommand::execute(){
try {
+ if (abort == true) { return 0; }
+
int count = 1;
- string binnames, name, sequence;
+ int error = 0;
//read fastafile
fasta->readFastaFile(in);
//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;
+
+ //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){
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
- string outputFileName = getRootName(globaldata->getListFile()) + list->getLabel() + ".fasta";
- openOutputFile(outputFileName, out);
-
- cout << list->getLabel() << '\t' << count << endl;
+ error = process(list, count);
+ 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)) {
+
+ error = process(lastList, count);
+ if (error == 1) { return 0; }
+
+ processedLabels.insert(lastList->getLabel());
+ userLabels.erase(lastList->getLabel());
- //for each bin in the list vector
- for (int i = 0; i < list->size(); i++) {
-
- 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 + '|' + 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();
}
- delete list;
+ if (count != 1) { delete lastList; }
+ lastList = list;
+
list = input->getListVector();
count++;
}
+
+ //output error messages about any remaining user labels
+ 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;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ error = process(lastList, count);
+ if (error == 1) { return 0; }
+ }
+
+ delete lastList;
return 0;
}
catch(exception& e) {
}
}
//**********************************************************************************************************************
+//return 1 if error, 0 otherwise
+int BinSeqCommand::process(ListVector* list, int count) {
+ try {
+ string binnames, name, sequence;
+ string outputFileName = getRootName(globaldata->getListFile()) + list->getLabel() + ".fasta";
+ openOutputFile(outputFileName, out);
+
+ cout << list->getLabel() << '\t' << count << endl;
+
+ //for each bin in the list vector
+ for (int i = 0; i < list->size(); i++) {
+ 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") {
+ cout << name << " is missing from your group file. Please correct. " << endl;
+ remove(outputFileName.c_str());
+ return 1;
+ }else{
+ name = name + "|" + group + "|" + 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 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") {
+ cout << binnames << " is missing from your group file. Please correct. " << endl;
+ remove(outputFileName.c_str());
+ return 1;
+ }else{
+ binnames = binnames + "|" + group + "|" + toString(i+1);
+ out << ">" << binnames << endl;
+ out << sequence << endl;
+ }
+ }
+ }else {
+ cout << binnames << " is missing from your fasta or name file. Please correct. " << endl;
+ remove(outputFileName.c_str());
+ return 1;
+ }
+ }
+
+ out.close();
+ return 0;
+
+ }
+ 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";
+ 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