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", "line", "label","group","sabund", "rabund"};
25 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
27 OptionParser parser(option);
28 map<string, string> parameters = parser.getParameters();
30 ValidParameters validParameter;
32 //check to make sure all parameters are valid for command
33 for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
34 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
37 globaldata->newRead();
39 //check for required parameters
40 listfile = validParameter.validFile(parameters, "list", true);
41 if (listfile == "not open") { abort = true; }
42 else if (listfile == "not found") { listfile = ""; }
43 else { globaldata->setListFile(listfile); globaldata->setFormat("list"); }
45 sabundfile = validParameter.validFile(parameters, "sabund", true);
46 if (sabundfile == "not open") { abort = true; }
47 else if (sabundfile == "not found") { sabundfile = ""; }
48 else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
50 rabundfile = validParameter.validFile(parameters, "rabund", true);
51 if (rabundfile == "not open") { abort = true; }
52 else if (rabundfile == "not found") { rabundfile = ""; }
53 else { globaldata->setRabundFile(rabundfile); globaldata->setFormat("rabund");}
55 sharedfile = validParameter.validFile(parameters, "shared", true);
56 if (sharedfile == "not open") { abort = true; }
57 else if (sharedfile == "not found") { sharedfile = ""; }
58 else { globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile"); }
60 groupfile = validParameter.validFile(parameters, "group", true);
61 if (groupfile == "not open") { abort = true; }
62 else if (groupfile == "not found") { groupfile = ""; }
64 globaldata->setGroupFile(groupfile);
65 groupMap = new GroupMap(groupfile);
67 globaldata->gGroupmap = groupMap;
70 //you are doing a list and group shared
71 if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); }
73 //you have not given a file
74 if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
75 mothurOut("You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. "); mothurOutEndLine(); abort = true;
78 //check for optional parameter and set defaults
79 // ...at some point should added some additional type checking...
80 line = validParameter.validFile(parameters, "line", false);
81 if (line == "not found") { line = ""; }
83 if(line != "all") { splitAtDash(line, lines); allLines = 0; }
84 else { allLines = 1; }
85 globaldata->lines = lines;
88 label = validParameter.validFile(parameters, "label", false);
89 if (label == "not found") { label = ""; }
91 if(label != "all") { splitAtDash(label, labels); allLines = 0; }
92 else { allLines = 1; }
93 globaldata->labels = labels;
96 globaldata->allLines = allLines;
98 //make sure user did not use both the line and label parameters
99 if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
101 orderfile = validParameter.validFile(parameters, "order", true);
102 if (orderfile == "not open") { abort = true; }
103 else if (orderfile == "not found") { orderfile = ""; }
104 else { globaldata->setOrderFile(orderfile); }
107 if (abort == false) {
108 //gets whichever one of the above is set
109 filename = globaldata->inputFileName;
115 catch(exception& e) {
116 errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
120 //**********************************************************************************************************************
122 void ReadOtuCommand::help(){
124 mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
125 mothurOut("collect.shared, rarefaction.shared or summary.shared command. Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
126 mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, line and label.\n");
127 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");
128 mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
129 mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
130 mothurOut("The line and label parameters are optional but you may not use both the line and label parameters at the same time.\n");
131 mothurOut("The label and line parameters are used to read specific lines in your input.\n");
132 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");
133 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");
134 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");
135 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");
136 mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
139 catch(exception& e) {
140 errorOut(e, "ReadOtuCommand", "help");
147 //**********************************************************************************************************************
149 ReadOtuCommand::~ReadOtuCommand(){
152 //**********************************************************************************************************************
154 int ReadOtuCommand::execute(){
157 if (abort == true) { return 0; }
159 if (globaldata->getFormat() == "shared") {
161 shared = new SharedCommand();
165 //change format to shared to speed up commands
166 globaldata->setFormat("sharedfile");
167 globaldata->setListFile("");
168 globaldata->setGroupFile("");
169 globaldata->setSharedFile(getRootName(filename) + "shared");
173 catch(exception& e) {
174 errorOut(e, "ReadOtuCommand", "execute");
178 //**********************************************************************************************************************