+++ /dev/null
-/*
- * binsequencecommand.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 4/3/09.
- * Copyright 2009 Schloss Lab UMASS Amhers. All rights reserved.
- *
- */
-
-#include "binsequencecommand.h"
-
-
-//**********************************************************************************************************************
-vector<string> BinSeqCommand::setParameters(){
- try {
- 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", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string BinSeqCommand::getHelpString(){
- try {
- 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";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "BinSeqCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-BinSeqCommand::BinSeqCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-BinSeqCommand::BinSeqCommand(string option) {
- try {
- abort = false; calledHelp = false;
- allLines = 1;
- labels.clear();
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- vector<string> myArray = setParameters();
-
- 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 (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
-
- //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("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()){
- 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") { //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; }
- else { m->setFastaFile(fastafile); }
-
- 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; }
- else { m->setListFile(listfile); }
-
- //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...
-
- label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; }
- else {
- if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
-
- namesfile = validParameter.validFile(parameters, "name", true);
- if (namesfile == "not open") { namesfile = ""; abort = true; }
- else if (namesfile == "not found") { namesfile = ""; }
- else { m->setNameFile(namesfile); }
-
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { abort = true; }
- else if (groupfile == "not found") { groupfile = ""; }
- else { m->setGroupFile(groupfile); }
-
- if (namesfile == ""){
- vector<string> files; files.push_back(fastafile);
- parser.getNameFile(files);
- }
-
- }
- }
- catch(exception& e) {
- m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-BinSeqCommand::~BinSeqCommand(){}
-//**********************************************************************************************************************
-
-int BinSeqCommand::execute(){
- try {
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- int error = 0;
-
- fasta = new FastaMap();
- if (groupfile != "") {
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
- }
-
- //read fastafile
- fasta->readFastaFile(fastafile);
-
- //if user gave a namesfile then use it
- if (namesfile != "") {
- readNamesFile();
- }
-
- input = new InputData(listfile, "list");
- list = input->getListVector();
- string lastLabel = list->getLabel();
-
- 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;
- set<string> userLabels = labels;
-
-
- while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
- }
-
- if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = list->getLabel();
-
- delete list;
- list = input->getListVector(lastLabel);
-
- error = process(list);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } 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();
- }
-
- if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } 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++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- if (list != NULL) { delete list; }
- list = input->getListVector(lastLabel);
-
- error = process(list);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
-
- delete list;
- }
-
- delete input;
- delete fasta;
- if (groupfile != "") { delete groupMap; }
-
- if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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) {
- m->errorOut(e, "BinSeqCommand", "execute");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-void BinSeqCommand::readNamesFile() {
- try {
- vector<string> dupNames;
- m->openInputFile(namesfile, inNames);
-
- string name, names, sequence;
-
- while(inNames){
- inNames >> name; //read from first column A
- inNames >> names; //read from second column A,B,C,D
-
- dupNames.clear();
-
- //parse names into vector
- m->splitAtComma(names, dupNames);
-
- //store names in fasta map
- sequence = fasta->getSequence(name);
- for (int i = 0; i < dupNames.size(); i++) {
- fasta->push_back(dupNames[i], sequence);
- }
-
- m->gobble(inNames);
- }
- inNames.close();
-
- }
- catch(exception& e) {
- m->errorOut(e, "BinSeqCommand", "readNamesFile");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-//return 1 if error, 0 otherwise
-int BinSeqCommand::process(ListVector* list) {
- try {
- string binnames, name, sequence;
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".fasta";
- m->openOutputFile(outputFileName, out);
-
- //save to output list of output file names
- outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
-
- 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(','));
- 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 + "\t" + toString(i+1);
- out << ">" << name << endl;
- out << sequence << endl;
- }else {//if you do have groups
- string group = groupMap->getGroup(name);
- if (group == "not found") {
- m->mothurOut(name + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
- return 1;
- }else{
- name = name + "\t" + group + "\t" + toString(i+1);
- out << ">" << name << endl;
- out << sequence << endl;
- }
- }
- }else {
- m->mothurOut(name + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
- return 1;
- }
-
- }
-
- //get last name
- sequence = fasta->getSequence(binnames);
- if (sequence != "not found") {
- //if you don't have groups
- if (groupfile == "") {
- binnames = binnames + "\t" + toString(i+1);
- out << ">" << binnames << endl;
- out << sequence << endl;
- }else {//if you do have groups
- string group = groupMap->getGroup(binnames);
- if (group == "not found") {
- m->mothurOut(binnames + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
- return 1;
- }else{
- binnames = binnames + "\t" + group + "\t" + toString(i+1);
- out << ">" << binnames << endl;
- out << sequence << endl;
- }
- }
- }else {
- m->mothurOut(binnames + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
- return 1;
- }
- }
-
- out.close();
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "BinSeqCommand", "process");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-
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