X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=getsharedotucommand.cpp;h=9302d1d21dfc52dbe295754e38aa86de55e0a4cc;hp=6ca4ee2d3dd5630c1ee38efaffe268a1e5f130c3;hb=499f4ac6e321f9f03d4c3aa25c3b6880892c8b83;hpb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18 diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp index 6ca4ee2..9302d1d 100644 --- a/getsharedotucommand.cpp +++ b/getsharedotucommand.cpp @@ -8,54 +8,86 @@ */ #include "getsharedotucommand.h" - +#include "sharedutilities.h" //********************************************************************************************************************** -vector GetSharedOTUCommand::getValidParameters(){ +vector GetSharedOTUCommand::setParameters(){ try { - string Array[] = {"label","unique","shared","fasta","list","group","output","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter pfasta("fasta", "InputTypes", "", "", "sharedFasta", "none", "none","fasta",false,false); parameters.push_back(pfasta); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "groupList","",false,false,true); parameters.push_back(pgroup); + CommandParameter plist("list", "InputTypes", "", "", "sharedList", "sharedList", "groupList","sharedseq",false,false,true); parameters.push_back(plist); + CommandParameter pshared("shared", "InputTypes", "", "", "sharedList-sharedFasta", "sharedList", "none","sharedseq",false,false,true); parameters.push_back(pshared); + CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "","",false,false); parameters.push_back(poutput); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter puniquegroups("uniquegroups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(puniquegroups); + CommandParameter psharedgroups("sharedgroups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(psharedgroups); + 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", "getValidParameters"); + m->errorOut(e, "GetSharedOTUCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -GetSharedOTUCommand::GetSharedOTUCommand(){ +string GetSharedOTUCommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["fasta"] = tempOutNames; - outputTypes["accnos"] = tempOutNames; - outputTypes["sharedseqs"] = tempOutNames; + string helpString = ""; + helpString += "The get.sharedseqs command parameters are list, group, shared, label, uniquegroups, sharedgroups, output and fasta. The list and group or shared 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 uniquegroups and sharedgroups 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 uniquegroups parameter mothur will return the otus that contain ONLY sequences from those groups.\n"; + helpString += "If you enter your groups under the sharedgroups 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 or shared 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. It can only be used with a list and group file not the shared file input.\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, uniquegroups=yourGroups, fasta=yourFastafile, output=yourOutput).\n"; + helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=amazon.groups, uniquegroups=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", "GetSharedOTUCommand"); + m->errorOut(e, "GetSharedOTUCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector GetSharedOTUCommand::getRequiredParameters(){ - try { - string Array[] = {"list","group"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "GetSharedOTUCommand", "getRequiredParameters"); - exit(1); - } +string GetSharedOTUCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "fasta") { pattern = "[filename],[distance],[group],shared.fasta"; } + else if (type == "accnos") { pattern = "[filename],[distance],[group],accnos"; } + else if (type == "sharedseqs") { pattern = "[filename],[distance],[group],shared.seqs"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "GetSharedOTUCommand", "getOutputPattern"); + exit(1); + } } //********************************************************************************************************************** -vector GetSharedOTUCommand::getRequiredFiles(){ +GetSharedOTUCommand::GetSharedOTUCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["accnos"] = tempOutNames; + outputTypes["sharedseqs"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "GetSharedOTUCommand", "getRequiredFiles"); + m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand"); exit(1); } } @@ -63,19 +95,16 @@ vector GetSharedOTUCommand::getRequiredFiles(){ GetSharedOTUCommand::GetSharedOTUCommand(string option) { try { - globaldata = GlobalData::getInstance(); abort = false; calledHelp = false; unique = true; 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 { - //valid paramters for this command - string Array[] = {"label","unique","shared","fasta","list","group","output","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -117,6 +146,14 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { //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("shared"); + //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["shared"] = inputDir + it->second; } + } it = parameters.find("group"); //user has given a template file @@ -131,15 +168,53 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { //check for required parameters listfile = validParameter.validFile(parameters, "list", true); if (listfile == "not open") { abort = true; } - else if (listfile == "not found") { listfile = ""; } - else { globaldata->setListFile(listfile); globaldata->setFormat("list"); } + else if (listfile == "not found") { listfile = ""; } + else { format = "list"; m->setListFile(listfile); } groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { abort = true; } else if (groupfile == "not found") { groupfile = ""; } - - if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; } - + else { m->setGroupFile(groupfile); } + + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { m->setSharedFile(sharedfile); } + + fastafile = validParameter.validFile(parameters, "fasta", true); + if (fastafile == "not open") { abort = true; } + else if (fastafile == "not found") { fastafile = ""; } + else { m->setFastaFile(fastafile); } + + + if ((sharedfile == "") && (listfile == "")) { //look for currents + //is there are current file available for either of these? + //give priority to shared, then list + sharedfile = m->getSharedFile(); + if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { + listfile = m->getListFile(); + if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a shared or list file."); m->mothurOutEndLine(); + abort = true; + } + } + }else if ((sharedfile != "") && (listfile != "")) { + m->mothurOut("You may enter ONLY ONE of the following: shared or list."); m->mothurOutEndLine(); abort = true; + } + + if (listfile != "") { + if (groupfile == ""){ + groupfile = m->getGroupFile(); + if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You need to provide a group file if you are going to use the list format."); m->mothurOutEndLine(); abort = true; + } + } + } + + if ((sharedfile != "") && (fastafile != "")) { m->mothurOut("You cannot use the fasta file with the shared file."); 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); @@ -151,30 +226,24 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { output = validParameter.validFile(parameters, "output", false); if (output == "not found") { output = ""; } + else if (output == "default") { output = ""; } - groups = validParameter.validFile(parameters, "unique", false); + groups = validParameter.validFile(parameters, "uniquegroups", false); if (groups == "not found") { groups = ""; } else { userGroups = "unique." + groups; m->splitAtDash(groups, Groups); - globaldata->Groups = Groups; - } - groups = validParameter.validFile(parameters, "shared", false); + groups = validParameter.validFile(parameters, "sharedgroups", false); if (groups == "not found") { groups = ""; } else { userGroups = groups; m->splitAtDash(groups, Groups); - globaldata->Groups = Groups; unique = false; } - fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = true; } - else if (fastafile == "not found") { fastafile = ""; } - - } + } } catch(exception& e) { @@ -184,156 +253,147 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { } //********************************************************************************************************************** -void GetSharedOTUCommand::help(){ - try { - m->mothurOut("The get.sharedseqs command parameters are list, group, label, unique, shared, output and fasta. The list and group parameters are required.\n"); - m->mothurOut("The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n"); - m->mothurOut("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"); - m->mothurOut("If you enter your groups under the unique parameter mothur will return the otus that contain ONLY sequences from those groups.\n"); - m->mothurOut("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"); - m->mothurOut("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"); - m->mothurOut("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"); - m->mothurOut("The output parameter allows you to output the list of names without the group and bin number added. \n"); - m->mothurOut("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"); - m->mothurOut("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"); - m->mothurOut("The get.sharedseqs command should be in the following format: get.sabund(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n"); - m->mothurOut("Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n"); - m->mothurOut("The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n"); - m->mothurOut("The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "GetSharedOTUCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -GetSharedOTUCommand::~GetSharedOTUCommand(){} - -//********************************************************************************************************************** - 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; } - - globaldata->gGroupmap = groupMap; - - if (Groups.size() == 0) { - Groups = groupMap->namesOfGroups; - - //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); - } - - //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++) { remove(outputNames[i].c_str()); } 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); - } + if ( sharedfile != "") { runShared(); } + else { + m->setGroups(Groups); + 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; + 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; } } - - 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(); - } + //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); } } - //run last label if you need to - if (needToRun == true) { - m->mothurOut(lastlist->getLabel()); - process(lastlist); - - processedLabels.insert(lastlist->getLabel()); - userLabels.erase(lastlist->getLabel()); + if (output == "accnos") { + itTypes = outputTypes.find("accnos"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); } + } } - - //reset groups parameter - globaldata->Groups.clear(); - - if (lastlist != NULL) { delete lastlist; } - - if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete groupMap; 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(); } @@ -358,19 +418,22 @@ int GetSharedOTUCommand::process(ListVector* shared) { 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"; - } + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile)); + variables["[distance]"] = shared->getLabel(); + variables["[group]"] = userGroups; + if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); } + else { outputFileNames = getOutputFileName("accnos", variables); } + m->openOutputFile(outputFileNames, outNames); bool wroteSomething = false; int num = 0; //go through each bin, find out if shared + vector binLabels = shared->getLabels(); for (int i = 0; i < shared->getNumBins(); i++) { - if (m->control_pressed) { outNames.close(); remove(outputFileNames.c_str()); return 0; } + if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; } bool uniqueOTU = true; @@ -381,15 +444,16 @@ int GetSharedOTUCommand::process(ListVector* shared) { 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()); + string names = shared->get(i); + vector binNames; + m->splitAtComma(names, binNames); + for(int j = 0; j < binNames.size(); j++) { + string name = binNames[j]; //find group string seqGroup = groupMap->getGroup(name); if (output != "accnos") { - namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i+1))); + namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + binLabels[i])); }else { namesOfSeqsInThisBin.push_back(name); } if (seqGroup == "not found") { m->mothurOut(name + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); } @@ -400,20 +464,6 @@ int GetSharedOTUCommand::process(ListVector* shared) { 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; @@ -448,7 +498,7 @@ int GetSharedOTUCommand::process(ListVector* shared) { outNames.close(); if (!wroteSomething) { - remove(outputFileNames.c_str()); + m->mothurRemove(outputFileNames); string outputString = "\t" + toString(num) + " - No otus shared by groups"; string groupString = ""; @@ -468,7 +518,8 @@ int GetSharedOTUCommand::process(ListVector* shared) { //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"; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile)); + string outputFileFasta = getOutputFileName("fasta", variables); ofstream outFasta; m->openOutputFile(outputFileFasta, outFasta); outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta); @@ -501,5 +552,206 @@ int GetSharedOTUCommand::process(ListVector* shared) { exit(1); } } +/***********************************************************/ +int GetSharedOTUCommand::runShared() { + try { + InputData input(sharedfile, "sharedfile"); + vector lookup = input.getSharedRAbundVectors(); + string lastLabel = lookup[0]->getLabel(); + + if (Groups.size() == 0) { + Groups = m->getGroups(); + + //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 allGroups = m->getAllGroups(); + util.setGroups(Groups, allGroups); + } + + //put groups in map to find easier + for(int i = 0; i < Groups.size(); i++) { + groupFinder[Groups[i]] = Groups[i]; + } + + //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; + + //as long as you are not at the end of the file or done wih the lines you want + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + if (m->control_pressed) { + outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; + } + + + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ + m->mothurOut(lookup[0]->getLabel()); + process(lookup); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + } + + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input.getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); + process(lookup); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); + } + + lastLabel = lookup[0]->getLabel(); + + //get next line to process + //prevent memory leak + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input.getSharedRAbundVectors(); + } + + if (m->control_pressed) { + outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; + } + + //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) { + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input.getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); + process(lookup); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + } + + //reset groups parameter + m->clearGroups(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetSharedOTUCommand", "runShared"); + exit(1); + } +} +/***********************************************************/ +int GetSharedOTUCommand::process(vector& lookup) { + try { + + string outputFileNames; + if (outputDir == "") { outputDir += m->hasPath(sharedfile); } + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)); + variables["[distance]"] = lookup[0]->getLabel(); + variables["[group]"] = userGroups; + if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); } + else { outputFileNames = getOutputFileName("accnos", variables); } + + ofstream outNames; + m->openOutputFile(outputFileNames, outNames); + + bool wroteSomething = false; + int num = 0; + + //go through each bin, find out if shared + for (int i = 0; i < lookup[0]->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; } + + set namesOfGroupsInThisBin; + + for(int j = 0; j < lookup.size(); j++) { + string seqGroup = lookup[j]->getGroup(); + string name = m->currentSharedBinLabels[i]; + + if (lookup[j]->getAbundance(i) != 0) { + if (output != "accnos") { + namesOfGroupsInThisBin.insert(name + "|" + seqGroup + "|" + toString(lookup[j]->getAbundance(i))); + }else { namesOfGroupsInThisBin.insert(name); } + + //is this seq in one of the groups we care about + it = groupFinder.find(seqGroup); + if (it == groupFinder.end()) { uniqueOTU = false; } //you have sequences 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 (set::iterator itNames = namesOfGroupsInThisBin.begin(); itNames != namesOfGroupsInThisBin.end(); itNames++) { + outNames << (*itNames) << endl; + } + } + } + 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); } + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "GetSharedOTUCommand", "process"); + exit(1); + } +} //**********************************************************************************************************************