X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsharedotucommand.cpp;h=9beca6aa96f75a58891b5326b5cbd94209701656;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=4fe711e568728f0fa1af026bec4c21af822732cd;hpb=348de0f8b17d84ede77081dcf67bd6ef43496677;p=mothur.git diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp index 4fe711e..9beca6a 100644 --- a/getsharedotucommand.cpp +++ b/getsharedotucommand.cpp @@ -8,54 +8,91 @@ */ #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", "", "", "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", "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, 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", "GetSharedOTUCommand"); + m->errorOut(e, "GetSharedOTUCommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector GetSharedOTUCommand::getRequiredParameters(){ +string GetSharedOTUCommand::getOutputFileNameTag(string type, string inputName=""){ try { - string Array[] = {"list","group"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "fasta") { outputFileName = "shared.fasta"; } + else if (type == "accnos") { outputFileName = "accnos"; } + else if (type == "sharedseqs") { outputFileName = "shared.seqs"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; } catch(exception& e) { - m->errorOut(e, "GetSharedOTUCommand", "getRequiredParameters"); + m->errorOut(e, "GetSharedOTUCommand", "getOutputFileNameTag"); 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 +100,16 @@ 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(); @@ -131,12 +165,25 @@ 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 = 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 = ""; } + 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; } @@ -151,13 +198,14 @@ 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); if (groups == "not found") { groups = ""; } else { userGroups = "unique." + groups; m->splitAtDash(groups, Groups); - globaldata->Groups = Groups; + m->setGroups(Groups); } @@ -166,14 +214,14 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option) { else { userGroups = groups; m->splitAtDash(groups, Groups); - globaldata->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); } } } @@ -184,36 +232,6 @@ 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.sharedseqs(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 { @@ -225,15 +243,19 @@ int GetSharedOTUCommand::execute(){ if (m->control_pressed) { delete groupMap; return 0; } - globaldata->gGroupmap = groupMap; - if (Groups.size() == 0) { - Groups = groupMap->namesOfGroups; + 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 @@ -269,7 +291,7 @@ int GetSharedOTUCommand::execute(){ if (m->control_pressed) { if (lastlist != NULL) { delete lastlist; } - for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); delete groupMap; return 0; } @@ -328,11 +350,11 @@ int GetSharedOTUCommand::execute(){ //reset groups parameter - globaldata->Groups.clear(); + m->clearGroups(); 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; } + 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 = ""; @@ -373,9 +395,9 @@ int GetSharedOTUCommand::process(ListVector* shared) { if (outputDir == "") { outputDir += m->hasPath(listfile); } if (output != "accnos") { - outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs"; + outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("sharedseqs"); }else { - outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos"; + outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("accnos"); } m->openOutputFile(outputFileNames, outNames); @@ -384,7 +406,7 @@ int GetSharedOTUCommand::process(ListVector* shared) { //go through each bin, find out if shared 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; @@ -462,7 +484,7 @@ 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 = ""; @@ -482,7 +504,7 @@ 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"; + string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("fasta"); ofstream outFasta; m->openOutputFile(outputFileFasta, outFasta); outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);