X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=binsequencecommand.cpp;h=7798a4d74f749eed04d4554c796776a58697b98b;hp=274a8901db3c8f17ad7e70519916c009e5613193;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0 diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp index 274a890..7798a4d 100644 --- a/binsequencecommand.cpp +++ b/binsequencecommand.cpp @@ -9,21 +9,88 @@ #include "binsequencecommand.h" + +//********************************************************************************************************************** +vector BinSeqCommand::setParameters(){ + try { + CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(plist); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount); + CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); 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 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, count, 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); + } +} +//********************************************************************************************************************** +string BinSeqCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "fasta") { pattern = "[filename],[distance],fasta"; } //makes file like: amazon.0.03.fasta + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "BinSeqCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** +BinSeqCommand::BinSeqCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "BinSeqCommand", "BinSeqCommand"); + exit(1); + } +} //********************************************************************************************************************** BinSeqCommand::BinSeqCommand(string option) { try { - globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; allLines = 1; labels.clear(); //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string AlignArray[] = {"fasta","label","name", "group","outputdir","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -36,19 +103,9 @@ BinSeqCommand::BinSeqCommand(string option) { 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() == "") { - m->mothurOut("You must read a listfile before running the bin.seqs command."); - m->mothurOutEndLine(); - abort = true; - } + //initialize outputTypes + vector 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); @@ -58,15 +115,23 @@ BinSeqCommand::BinSeqCommand(string option) { it = parameters.find("fasta"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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 = hasPath(it->second); + 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; } } @@ -74,17 +139,46 @@ BinSeqCommand::BinSeqCommand(string option) { it = parameters.find("group"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + 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; } } + + it = parameters.find("count"); + //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["count"] = inputDir + it->second; } + } } //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; } + 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... @@ -92,35 +186,40 @@ BinSeqCommand::BinSeqCommand(string option) { 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; } } - //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; } + 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); } + + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { countfile = ""; abort = true; } + else if (countfile == "not found") { countfile = ""; } + else { m->setCountTableFile(countfile); } + + if ((namesfile != "") && (countfile != "")) { + m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true; + } + + if ((groupfile != "") && (countfile != "")) { + m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true; + } + + if (countfile == "") { + if (namesfile == ""){ + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } + } - if (abort == false) { -// 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) { @@ -130,65 +229,34 @@ BinSeqCommand::BinSeqCommand(string option) { } //********************************************************************************************************************** -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(){ try { - if (abort == true) { return 0; } + 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); - - //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); + if (namesfile != "") { readNamesFile(); } + if (countfile != "") { ct.readTable(countfile); } - input = globaldata->ginput; - list = globaldata->gListVector; + 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 processedLabels; set userLabels = labels; @@ -196,23 +264,25 @@ int BinSeqCommand::execute(){ 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) { return 0; } + 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 ((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); - if (error == 1) { return 0; } + 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()); @@ -227,7 +297,8 @@ int BinSeqCommand::execute(){ 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::iterator it; bool needToRun = false; @@ -247,11 +318,24 @@ int BinSeqCommand::execute(){ list = input->getListVector(lastLabel); error = process(list); - if (error == 1) { return 0; } + 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; } + + //set align file as new current fastafile + string currentFasta = ""; + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); } + } + m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } @@ -270,7 +354,7 @@ int BinSeqCommand::execute(){ void BinSeqCommand::readNamesFile() { try { vector dupNames; - openInputFile(namesfile, inNames); + m->openInputFile(namesfile, inNames); string name, names, sequence; @@ -281,7 +365,7 @@ void BinSeqCommand::readNamesFile() { dupNames.clear(); //parse names into vector - splitAtComma(names, dupNames); + m->splitAtComma(names, dupNames); //store names in fasta map sequence = fasta->getSequence(name); @@ -289,7 +373,7 @@ void BinSeqCommand::readNamesFile() { fasta->push_back(dupNames[i], sequence); } - gobble(inNames); + m->gobble(inNames); } inNames.close(); @@ -303,81 +387,75 @@ void BinSeqCommand::readNamesFile() { //return 1 if error, 0 otherwise int BinSeqCommand::process(ListVector* list) { try { - string binnames, name, sequence; - - string outputFileName = outputDir + getRootName(getSimpleName(globaldata->getListFile())) + list->getLabel() + ".fasta"; - openOutputFile(outputFileName, out); - - //save to output list of output file names - outputNames.push_back(outputFileName); - - m->mothurOut(list->getLabel()); m->mothurOutEndLine(); - - //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") { - m->mothurOut(name + " is missing from your group file. Please correct. "); m->mothurOutEndLine(); - remove(outputFileName.c_str()); - return 1; - }else{ - name = name + "|" + group + "|" + 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(); - 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") { - m->mothurOut(binnames + " is missing from your group file. Please correct. "); m->mothurOutEndLine(); - remove(outputFileName.c_str()); - return 1; - }else{ - binnames = binnames + "|" + group + "|" + 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(); - remove(outputFileName.c_str()); - return 1; - } - } - - out.close(); - return 0; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); + variables["[distance]"] = list->getLabel(); + string outputFileName = getOutputFileName("fasta", variables); + + m->openOutputFile(outputFileName, out); + 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; } + + string binnames = list->get(i); + vector names; + m->splitAtComma(binnames, names); + for (int j = 0; j < names.size(); j++) { + string name = names[j]; + + //do work for that name + string sequence = fasta->getSequence(name); + + if (countfile != "") { + if (sequence != "not found") { + if (ct.hasGroupInfo()) { + vector groups = ct.getGroups(name); + string groupInfo = ""; + for (int k = 0; k < groups.size()-1; k++) { + groupInfo += groups[k] + "-"; + } + if (groups.size() != 0) { groupInfo += groups[groups.size()-1]; } + else { groupInfo = "not found"; } + name = name + "\t" + groupInfo + "\t" + toString(i+1)+ "\tNumRep=" + toString(ct.getNumSeqs(name)); + out << ">" << name << endl; + out << sequence << endl; + }else { + name = name + "\t" + toString(i+1) + "\tNumRep=" + toString(ct.getNumSeqs(name)); + out << ">" << name << endl; + out << sequence << endl; + } + + }else { m->mothurOut(name + " is missing from your fasta. Does your list file contain all sequence names or just the uniques?"); m->mothurOutEndLine(); return 1; } + }else { + 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; } + } + } + } + + out.close(); + return 0; } catch(exception& e) {