X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readotucommand.cpp;h=30dc55343d46e0656c7123aba7afddea7f4b3a77;hb=7a8fc1115b3871107c09a4b9b307b1f2ab7d3fcf;hp=999d8de95ecdda62b411e3d5fab11092d3105636;hpb=462fca6d24fd15ca035358ff70bcfae52c3281c3;p=mothur.git diff --git a/readotucommand.cpp b/readotucommand.cpp index 999d8de..30dc553 100644 --- a/readotucommand.cpp +++ b/readotucommand.cpp @@ -10,7 +10,7 @@ #include "readotucommand.h" //********************************************************************************************************************** -ReadOtuCommand::ReadOtuCommand(string option){ +ReadOtuCommand::ReadOtuCommand(string option) { try { globaldata = GlobalData::getInstance(); abort = false; @@ -21,21 +21,81 @@ ReadOtuCommand::ReadOtuCommand(string option){ else { //valid paramters for this command - string Array[] = {"list","order","shared", "line", "label","group","sabund", "rabund"}; + string Array[] = {"list","order","shared", "label","group","sabund", "rabund","groups","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); map parameters = parser.getParameters(); ValidParameters validParameter; + map::iterator it; //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } - + globaldata->newRead(); + //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("list"); + //user has given a template file + if(it != parameters.end()){ + path = 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("order"); + //user has given a template file + if(it != parameters.end()){ + path = hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["order"] = inputDir + it->second; } + } + + it = parameters.find("shared"); + //user has given a template file + if(it != parameters.end()){ + path = 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 + if(it != parameters.end()){ + path = 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("sabund"); + //user has given a template file + if(it != parameters.end()){ + path = hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["sabund"] = inputDir + it->second; } + } + + it = parameters.find("rabund"); + //user has given a template file + if(it != parameters.end()){ + path = hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["rabund"] = inputDir + it->second; } + } + + } + + + //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 = ""; } + //check for required parameters listfile = validParameter.validFile(parameters, "list", true); if (listfile == "not open") { abort = true; } @@ -63,28 +123,30 @@ ReadOtuCommand::ReadOtuCommand(string option){ else { globaldata->setGroupFile(groupfile); groupMap = new GroupMap(groupfile); - groupMap->readMap(); + + int error = groupMap->readMap(); + if (error == 1) { abort = true; } + globaldata->gGroupmap = groupMap; } + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + splitAtDash(groups, Groups); + globaldata->Groups = Groups; + } //you are doing a list and group shared if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); } //you have not given a file if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) { - mothurOut("You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. "); mothurOutEndLine(); abort = true; + m->mothurOut("You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. "); m->mothurOutEndLine(); abort = true; } //check for optional parameter and set defaults // ...at some point should added some additional type checking... - line = validParameter.validFile(parameters, "line", false); - if (line == "not found") { line = ""; } - else { - if(line != "all") { splitAtDash(line, lines); allLines = 0; } - else { allLines = 1; } - globaldata->lines = lines; - } - label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; } else { @@ -94,26 +156,22 @@ ReadOtuCommand::ReadOtuCommand(string option){ } globaldata->allLines = allLines; - - //make sure user did not use both the line and label parameters - if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; } - + orderfile = validParameter.validFile(parameters, "order", true); if (orderfile == "not open") { abort = true; } else if (orderfile == "not found") { orderfile = ""; } else { globaldata->setOrderFile(orderfile); } - + if (abort == false) { //gets whichever one of the above is set filename = globaldata->inputFileName; } - } } catch(exception& e) { - errorOut(e, "ReadOtuCommand", "ReadOtuCommand"); + m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand"); exit(1); } } @@ -121,23 +179,23 @@ ReadOtuCommand::ReadOtuCommand(string option){ void ReadOtuCommand::help(){ try { - mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n"); - mothurOut("collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n"); - mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label.\n"); - mothurOut("The read.otu command can be used in two ways. The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single.\n"); - mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n"); - mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n"); - mothurOut("The line and label parameters are optional but you may not use both the line and label parameters at the same time.\n"); - mothurOut("The label and line parameters are used to read specific lines in your input.\n"); - mothurOut("The second way to use the read.otu command is to read a list and a group, or a shared so you can use the collect.shared, rarefaction.shared or summary.shared commands.\n"); - mothurOut("In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile, line=yourLines) or read.otu(shared=yourSharedFile). \n"); - mothurOut("The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file read.otu command parses the .list file\n"); - mothurOut("and separates it into groups. It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .list file for each group. \n"); - mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n"); + m->mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n"); + m->mothurOut("collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n"); + m->mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, label and groups.\n"); + m->mothurOut("The read.otu command can be used in two ways. The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single.\n"); + m->mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n"); + m->mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n"); + m->mothurOut("The label parameter is used to read specific labels in your input.\n"); + m->mothurOut("The second way to use the read.otu command is to read a list and a group, or a shared so you can use the collect.shared, rarefaction.shared or summary.shared commands.\n"); + m->mothurOut("In this case the read.otu command should be in the following format: read.otu(list=yourListFile, group=yourGroupFile) or read.otu(shared=yourSharedFile). \n"); + m->mothurOut("The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file read.otu command parses the .list file\n"); + m->mothurOut("and separates it into groups. It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .rabund file for each group. \n"); + m->mothurOut("You can use the groups parameter to choose only specific groups to be used in the .shared and .rabund files. \n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n"); } catch(exception& e) { - errorOut(e, "ReadOtuCommand", "help"); + m->errorOut(e, "ReadOtuCommand", "help"); exit(1); } } @@ -145,41 +203,37 @@ void ReadOtuCommand::help(){ //********************************************************************************************************************** - -ReadOtuCommand::~ReadOtuCommand(){ - } - +ReadOtuCommand::~ReadOtuCommand(){} //********************************************************************************************************************** int ReadOtuCommand::execute(){ try { if (abort == true) { return 0; } - + if (globaldata->getFormat() == "shared") { - shared = new SharedCommand(); + shared = new SharedCommand(outputDir); int okay = shared->execute(); - delete shared; //problem with shared if (okay == 1) { globaldata->setListFile(""); globaldata->setGroupFile(""); globaldata->setSharedFile(""); - }else{ - - //change format to shared to speed up commands - globaldata->setFormat("sharedfile"); - globaldata->setListFile(""); - globaldata->setGroupFile(""); - globaldata->setSharedFile(getRootName(filename) + "shared"); + }else { //shared command outputs the filenames + //m->mothurOutEndLine(); + //m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine(); + //m->mothurOutEndLine(); } + + delete shared; } return 0; } catch(exception& e) { - errorOut(e, "ReadOtuCommand", "execute"); + m->errorOut(e, "ReadOtuCommand", "execute"); exit(1); } }