X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=getsharedotucommand.cpp;fp=getsharedotucommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=02d8413675bade0cf79f8781987cc45078b74db2;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp deleted file mode 100644 index 02d8413..0000000 --- a/getsharedotucommand.cpp +++ /dev/null @@ -1,518 +0,0 @@ -/* - * getsharedotucommand.cpp - * Mothur - * - * Created by westcott on 9/22/09. - * Copyright 2009 Schloss Lab. All rights reserved. - * - */ - -#include "getsharedotucommand.h" -#include "sharedutilities.h" - -//********************************************************************************************************************** -vector GetSharedOTUCommand::setParameters(){ - try { - CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta); - CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(pgroup); - CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(plist); - CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "",false,false); parameters.push_back(poutput); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter punique("unique", "String", "", "", "", "", "",false,false); parameters.push_back(punique); - CommandParameter pshared("shared", "String", "", "", "", "", "",false,false); parameters.push_back(pshared); - 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, "GetSharedOTUCommand", "setParameters"); - exit(1); - } -} -//********************************************************************************************************************** -string GetSharedOTUCommand::getHelpString(){ - try { - string helpString = ""; - helpString += "The get.sharedseqs command parameters are list, group, label, unique, shared, output and fasta. The list and group parameters are required, unless you have valid current files.\n"; - helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n"; - helpString += "The unique and shared parameters allow you to select groups you would like to know the shared info for, and are separated by dashes.\n"; - helpString += "If you enter your groups under the unique parameter mothur will return the otus that contain ONLY sequences from those groups.\n"; - helpString += "If you enter your groups under the shared parameter mothur will return the otus that contain sequences from those groups and may also contain sequences from other groups.\n"; - helpString += "If you do not enter any groups then the get.sharedseqs command will return sequences that are unique to all groups in your group file.\n"; - helpString += "The fasta parameter allows you to input a fasta file and outputs a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified.\n"; - helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n"; - helpString += "With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n"; - helpString += "The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n"; - helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(list=yourListFile, group=yourGroupFile, label=yourLabels, unique=yourGroups, fasta=yourFastafile, output=yourOutput).\n"; - helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group= amazon.groups, unique=forest-pasture, fasta=amazon.fasta, output=accnos).\n"; - helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n"; - helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n"; - helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n"; - return helpString; - } - catch(exception& e) { - m->errorOut(e, "GetSharedOTUCommand", "getHelpString"); - exit(1); - } -} -//********************************************************************************************************************** -GetSharedOTUCommand::GetSharedOTUCommand(){ - try { - abort = true; calledHelp = true; - setParameters(); - vector tempOutNames; - outputTypes["fasta"] = tempOutNames; - outputTypes["accnos"] = tempOutNames; - outputTypes["sharedseqs"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand"); - exit(1); - } -} -//********************************************************************************************************************** -GetSharedOTUCommand::GetSharedOTUCommand(string option) { - try { - - abort = false; calledHelp = false; - unique = true; - allLines = 1; - - //allow user to run help - if(option == "help") { help(); abort = true; calledHelp = true; } - else if(option == "citation") { citation(); abort = true; calledHelp = true;} - - else { - vector myArray = setParameters(); - - OptionParser parser(option); - map parameters = parser.getParameters(); - - ValidParameters validParameter; - map::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 tempOutNames; - outputTypes["fasta"] = tempOutNames; - outputTypes["accnos"] = tempOutNames; - outputTypes["sharedseqs"] = tempOutNames; - - //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 = ""; } - - //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("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 - listfile = validParameter.validFile(parameters, "list", true); - if (listfile == "not open") { abort = true; } - else if (listfile == "not found") { - listfile = m->getListFile(); - if (listfile != "") { format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } - else { - m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine(); - abort = true; - } - }else { format = "list"; m->setListFile(listfile); } - - groupfile = validParameter.validFile(parameters, "group", true); - if (groupfile == "not open") { abort = true; } - else if (groupfile == "not found") { - groupfile = m->getGroupFile(); - if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); } - else { - m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine(); - abort = true; - } - }else { m->setGroupFile(groupfile); } - - if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; } - - //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; } - } - - output = validParameter.validFile(parameters, "output", false); - if (output == "not found") { output = ""; } - else if (output == "default") { output = ""; } - - groups = validParameter.validFile(parameters, "unique", false); - if (groups == "not found") { groups = ""; } - else { - userGroups = "unique." + groups; - m->splitAtDash(groups, Groups); - m->setGroups(Groups); - - } - - groups = validParameter.validFile(parameters, "shared", false); - if (groups == "not found") { groups = ""; } - else { - userGroups = groups; - m->splitAtDash(groups, Groups); - m->setGroups(Groups); - unique = false; - } - - fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = true; } - else if (fastafile == "not found") { fastafile = ""; } - else { m->setFastaFile(fastafile); } - } - - } - catch(exception& e) { - m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand"); - exit(1); - } -} -//********************************************************************************************************************** - -int GetSharedOTUCommand::execute(){ - try { - - if (abort == true) { if (calledHelp) { return 0; } return 2; } - - groupMap = new GroupMap(groupfile); - int error = groupMap->readMap(); - if (error == 1) { delete groupMap; return 0; } - - if (m->control_pressed) { delete groupMap; return 0; } - - if (Groups.size() == 0) { - Groups = groupMap->getNamesOfGroups(); - - //make string for outputfile name - userGroups = "unique."; - for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; } - userGroups = userGroups.substr(0, userGroups.length()-1); - }else{ - //sanity check for group names - SharedUtil util; - vector namesOfGroups = groupMap->getNamesOfGroups(); - util.setGroups(Groups, namesOfGroups); - groupMap->setNamesOfGroups(namesOfGroups); - } - - //put groups in map to find easier - for(int i = 0; i < Groups.size(); i++) { - groupFinder[Groups[i]] = Groups[i]; - } - - if (fastafile != "") { - ifstream inFasta; - m->openInputFile(fastafile, inFasta); - - while(!inFasta.eof()) { - if (m->control_pressed) { outputTypes.clear(); inFasta.close(); delete groupMap; return 0; } - - Sequence seq(inFasta); m->gobble(inFasta); - if (seq.getName() != "") { seqs.push_back(seq); } - } - inFasta.close(); - } - - ListVector* lastlist = NULL; - string lastLabel = ""; - - //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; - - ifstream in; - m->openInputFile(listfile, in); - - //as long as you are not at the end of the file or done wih the lines you want - while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) { - - if (m->control_pressed) { - if (lastlist != NULL) { delete lastlist; } - for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); - delete groupMap; return 0; - } - - list = new ListVector(in); - - if(allLines == 1 || labels.count(list->getLabel()) == 1){ - m->mothurOut(list->getLabel()); - process(list); - - processedLabels.insert(list->getLabel()); - userLabels.erase(list->getLabel()); - } - - if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { - string saveLabel = list->getLabel(); - - m->mothurOut(lastlist->getLabel()); - process(lastlist); - - processedLabels.insert(lastlist->getLabel()); - userLabels.erase(lastlist->getLabel()); - - //restore real lastlabel to save below - list->setLabel(saveLabel); - } - - lastLabel = list->getLabel(); - - if (lastlist != NULL) { delete lastlist; } - lastlist = list; - } - - in.close(); - - //output error messages about any remaining user labels - set::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) { - m->mothurOut(lastlist->getLabel()); - process(lastlist); - - processedLabels.insert(lastlist->getLabel()); - userLabels.erase(lastlist->getLabel()); - } - - - //reset groups parameter - m->clearGroups(); - - if (lastlist != NULL) { delete lastlist; } - - if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete groupMap; return 0; } - - //set fasta file as new current fastafile - string current = ""; - itTypes = outputTypes.find("fasta"); - if (itTypes != outputTypes.end()) { - if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } - } - - if (output == "accnos") { - itTypes = outputTypes.find("accnos"); - if (itTypes != outputTypes.end()) { - if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); } - } - } - - 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, "GetSharedOTUCommand", "execute"); - exit(1); - } -} -/***********************************************************/ -int GetSharedOTUCommand::process(ListVector* shared) { - try { - - map fastaMap; - - ofstream outNames; - string outputFileNames; - - if (outputDir == "") { outputDir += m->hasPath(listfile); } - if (output != "accnos") { - outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs"; - }else { - outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos"; - } - m->openOutputFile(outputFileNames, outNames); - - bool wroteSomething = false; - int num = 0; - - //go through each bin, find out if shared - for (int i = 0; i < shared->getNumBins(); i++) { - if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; } - - bool uniqueOTU = true; - - map atLeastOne; - for (int f = 0; f < Groups.size(); f++) { - atLeastOne[Groups[f]] = 0; - } - - vector namesOfSeqsInThisBin; - - string names = shared->get(i); - while ((names.find_first_of(',') != -1)) { - string name = names.substr(0,names.find_first_of(',')); - names = names.substr(names.find_first_of(',')+1, names.length()); - - //find group - string seqGroup = groupMap->getGroup(name); - if (output != "accnos") { - namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i+1))); - }else { namesOfSeqsInThisBin.push_back(name); } - - if (seqGroup == "not found") { m->mothurOut(name + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); } - - //is this seq in one of hte groups we care about - it = groupFinder.find(seqGroup); - if (it == groupFinder.end()) { uniqueOTU = false; } //you have a sequence from a group you don't want - else { atLeastOne[seqGroup]++; } - } - - //get last name - string seqGroup = groupMap->getGroup(names); - if (output != "accnos") { - namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1))); - }else { namesOfSeqsInThisBin.push_back(names); } - - if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); } - - //is this seq in one of hte groups we care about - it = groupFinder.find(seqGroup); - if (it == groupFinder.end()) { uniqueOTU = false; } //you have a sequence from a group you don't want - else { atLeastOne[seqGroup]++; } - - - //make sure you have at least one seq from each group you want - bool sharedByAll = true; - map::iterator it2; - for (it2 = atLeastOne.begin(); it2 != atLeastOne.end(); it2++) { - if (it2->second == 0) { sharedByAll = false; } - } - - //if the user wants unique bins and this is unique then print - //or this the user wants shared bins and this bin is shared then print - if ((unique && uniqueOTU && sharedByAll) || (!unique && sharedByAll)) { - - wroteSomething = true; - num++; - - //output list of names - for (int j = 0; j < namesOfSeqsInThisBin.size(); j++) { - outNames << namesOfSeqsInThisBin[j] << endl; - - if (fastafile != "") { - if (output != "accnos") { - string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('|')); - seqName = seqName.substr(0,seqName.find_last_of('|')); - fastaMap[seqName] = namesOfSeqsInThisBin[j]; //fastaMap needs to contain just the seq name for output later - }else { - fastaMap[namesOfSeqsInThisBin[j]] = namesOfSeqsInThisBin[j]; - } - } - } - } - } - - outNames.close(); - - if (!wroteSomething) { - m->mothurRemove(outputFileNames); - string outputString = "\t" + toString(num) + " - No otus shared by groups"; - - string groupString = ""; - for (int h = 0; h < Groups.size(); h++) { - groupString += " " + Groups[h]; - } - - outputString += groupString + "."; - m->mothurOut(outputString); m->mothurOutEndLine(); - }else { - m->mothurOut("\t" + toString(num)); m->mothurOutEndLine(); - outputNames.push_back(outputFileNames); - if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); } - else { outputTypes["accnos"].push_back(outputFileNames); } - } - - //if fasta file provided output new fasta file - if ((fastafile != "") && wroteSomething) { - if (outputDir == "") { outputDir += m->hasPath(fastafile); } - string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta"; - ofstream outFasta; - m->openOutputFile(outputFileFasta, outFasta); - outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta); - - for (int k = 0; k < seqs.size(); k++) { - if (m->control_pressed) { outFasta.close(); return 0; } - - //if this is a sequence we want, output it - it = fastaMap.find(seqs[k].getName()); - if (it != fastaMap.end()) { - - if (output != "accnos") { - outFasta << ">" << it->second << endl; - }else { - outFasta << ">" << it->first << endl; - } - - outFasta << seqs[k].getAligned() << endl; - } - } - - outFasta.close(); - } - - return 0; - - } - catch(exception& e) { - m->errorOut(e, "GetSharedOTUCommand", "process"); - exit(1); - } -} - -//**********************************************************************************************************************