5 * Created by Sarah Westcott on 1/20/09.
6 * Copyright 2009 Schloss Lab UMASS AMherst. All rights reserved.
10 #include "readotucommand.h"
12 //**********************************************************************************************************************
13 ReadOtuCommand::ReadOtuCommand(string option){
15 globaldata = GlobalData::getInstance();
19 //allow user to run help
20 if(option == "help") { help(); abort = true; }
23 //valid paramters for this command
24 string Array[] = {"list","order","shared", "label","group","sabund", "rabund","groups","outputdir","inputdir"};
25 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
27 OptionParser parser(option);
28 map<string, string> parameters = parser.getParameters();
30 ValidParameters validParameter;
31 map<string, string>::iterator it;
33 //check to make sure all parameters are valid for command
34 for (it = parameters.begin(); it != parameters.end(); it++) {
35 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
38 globaldata->newRead();
40 //if the user changes the input directory command factory will send this info to us in the output parameter
41 string inputDir = validParameter.validFile(parameters, "inputdir", false);
42 if (inputDir == "not found"){ inputDir = ""; }
45 it = parameters.find("list");
46 //user has given a template file
47 if(it != parameters.end()){
48 path = hasPath(it->second);
49 //if the user has not given a path then, add inputdir. else leave path alone.
50 if (path == "") { parameters["list"] = inputDir + it->second; }
53 it = parameters.find("order");
54 //user has given a template file
55 if(it != parameters.end()){
56 path = hasPath(it->second);
57 //if the user has not given a path then, add inputdir. else leave path alone.
58 if (path == "") { parameters["order"] = inputDir + it->second; }
61 it = parameters.find("shared");
62 //user has given a template file
63 if(it != parameters.end()){
64 path = hasPath(it->second);
65 //if the user has not given a path then, add inputdir. else leave path alone.
66 if (path == "") { parameters["shared"] = inputDir + it->second; }
69 it = parameters.find("group");
70 //user has given a template file
71 if(it != parameters.end()){
72 path = hasPath(it->second);
73 //if the user has not given a path then, add inputdir. else leave path alone.
74 if (path == "") { parameters["group"] = inputDir + it->second; }
77 it = parameters.find("sabund");
78 //user has given a template file
79 if(it != parameters.end()){
80 path = hasPath(it->second);
81 //if the user has not given a path then, add inputdir. else leave path alone.
82 if (path == "") { parameters["sabund"] = inputDir + it->second; }
85 it = parameters.find("rabund");
86 //user has given a template file
87 if(it != parameters.end()){
88 path = hasPath(it->second);
89 //if the user has not given a path then, add inputdir. else leave path alone.
90 if (path == "") { parameters["rabund"] = inputDir + it->second; }
96 //if the user changes the output directory command factory will send this info to us in the output parameter
97 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
99 //check for required parameters
100 listfile = validParameter.validFile(parameters, "list", true);
101 if (listfile == "not open") { abort = true; }
102 else if (listfile == "not found") { listfile = ""; }
103 else { globaldata->setListFile(listfile); globaldata->setFormat("list"); }
105 sabundfile = validParameter.validFile(parameters, "sabund", true);
106 if (sabundfile == "not open") { abort = true; }
107 else if (sabundfile == "not found") { sabundfile = ""; }
108 else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
110 rabundfile = validParameter.validFile(parameters, "rabund", true);
111 if (rabundfile == "not open") { abort = true; }
112 else if (rabundfile == "not found") { rabundfile = ""; }
113 else { globaldata->setRabundFile(rabundfile); globaldata->setFormat("rabund");}
115 sharedfile = validParameter.validFile(parameters, "shared", true);
116 if (sharedfile == "not open") { abort = true; }
117 else if (sharedfile == "not found") { sharedfile = ""; }
118 else { globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile"); }
120 groupfile = validParameter.validFile(parameters, "group", true);
121 if (groupfile == "not open") { abort = true; }
122 else if (groupfile == "not found") { groupfile = ""; }
124 globaldata->setGroupFile(groupfile);
125 groupMap = new GroupMap(groupfile);
127 int error = groupMap->readMap();
128 if (error == 1) { abort = true; }
130 globaldata->gGroupmap = groupMap;
133 groups = validParameter.validFile(parameters, "groups", false);
134 if (groups == "not found") { groups = ""; }
136 splitAtDash(groups, Groups);
137 globaldata->Groups = Groups;
140 //you are doing a list and group shared
141 if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); }
143 //you have not given a file
144 if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
145 mothurOut("You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. "); mothurOutEndLine(); abort = true;
148 //check for optional parameter and set defaults
149 // ...at some point should added some additional type checking...
150 label = validParameter.validFile(parameters, "label", false);
151 if (label == "not found") { label = ""; }
153 if(label != "all") { splitAtDash(label, labels); allLines = 0; }
154 else { allLines = 1; }
155 globaldata->labels = labels;
158 globaldata->allLines = allLines;
160 orderfile = validParameter.validFile(parameters, "order", true);
161 if (orderfile == "not open") { abort = true; }
162 else if (orderfile == "not found") { orderfile = ""; }
163 else { globaldata->setOrderFile(orderfile); }
166 if (abort == false) {
167 //gets whichever one of the above is set
168 filename = globaldata->inputFileName;
174 catch(exception& e) {
175 errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
179 //**********************************************************************************************************************
181 void ReadOtuCommand::help(){
183 mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
184 mothurOut("collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
185 mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, label and groups.\n");
186 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");
187 mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
188 mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
189 mothurOut("The label parameter is used to read specific labels in your input.\n");
190 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");
191 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");
192 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");
193 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");
194 mothurOut("You can use the groups parameter to choose only specific groups to be used in the .shared and .rabund files. \n");
195 mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
198 catch(exception& e) {
199 errorOut(e, "ReadOtuCommand", "help");
206 //**********************************************************************************************************************
208 ReadOtuCommand::~ReadOtuCommand(){
211 //**********************************************************************************************************************
213 int ReadOtuCommand::execute(){
216 if (abort == true) { return 0; }
218 if (globaldata->getFormat() == "shared") {
220 shared = new SharedCommand(outputDir);
221 int okay = shared->execute();
223 //problem with shared
225 globaldata->setListFile("");
226 globaldata->setGroupFile("");
227 globaldata->setSharedFile("");
234 catch(exception& e) {
235 errorOut(e, "ReadOtuCommand", "execute");
239 //**********************************************************************************************************************