--- /dev/null
+/*
+ * countseqscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 6/1/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "countseqscommand.h"
+#include "groupmap.h"
+#include "sharedutilities.h"
+
+//**********************************************************************************************************************
+vector<string> CountSeqsCommand::setParameters(){
+ try {
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string CountSeqsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The count.seqs command reads a name file and outputs a .count.summary file. You may also provide a group file to get the counts broken down by group.\n";
+ helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
+ helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
+ helpString += "The count.seqs command should be in the following format: count.seqs(name=yourNameFile).\n";
+ helpString += "Example count.seqs(name=amazon.names).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourNameFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+CountSeqsCommand::CountSeqsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "CountSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+CountSeqsCommand::CountSeqsCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
+
+ //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("name");
+ //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["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //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["group"] = inputDir + it->second; }
+ }
+ }
+
+ //check for required parameters
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found"){
+ namefile = m->getNameFile();
+ if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = "all"; }
+ m->splitAtDash(groups, Groups);
+
+ //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 = m->hasPath(namefile); }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "CountSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int CountSeqsCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ ofstream out;
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "count.summary";
+ m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName);
+ out << "Representative Sequence\t total\t";
+
+ GroupMap* groupMap;
+ if (groupfile != "") {
+ groupMap = new GroupMap(groupfile); groupMap->readMap();
+
+ //make sure groups are valid. takes care of user setting groupNames that are invalid or setting groups=all
+ SharedUtil* util = new SharedUtil();
+ util->setGroups(Groups, groupMap->namesOfGroups);
+ delete util;
+
+ //sort groupNames so that the group title match the counts below, this is needed because the map object automatically sorts
+ sort(Groups.begin(), Groups.end());
+
+ //print groupNames
+ for (int i = 0; i < Groups.size(); i++) {
+ out << Groups[i] << '\t';
+ }
+ }
+ out << endl;
+
+ //open input file
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ string firstCol, secondCol;
+ in >> firstCol >> secondCol; m->gobble(in);
+
+ vector<string> names;
+ m->splitAtChar(secondCol, names, ',');
+
+ if (groupfile != "") {
+ //set to 0
+ map<string, int> groupCounts;
+ int total = 0;
+ for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
+
+ //get counts for each of the users groups
+ for (int i = 0; i < names.size(); i++) {
+ string group = groupMap->getGroup(names[i]);
+
+ if (group == "not found") { m->mothurOut("[ERROR]: " + names[i] + " is not in your groupfile, please correct."); m->mothurOutEndLine(); }
+ else {
+ map<string, int>::iterator it = groupCounts.find(group);
+
+ //if not found, then this sequence is not from a group we care about
+ if (it != groupCounts.end()) {
+ it->second++;
+ total++;
+ }
+ }
+ }
+
+ if (total != 0) {
+ out << firstCol << '\t' << total << '\t';
+ for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
+ out << it->second << '\t';
+ }
+ out << endl;
+ }
+ }else {
+ out << firstCol << '\t' << names.size() << endl;
+ }
+
+
+ }
+ in.close();
+
+ if (groupfile != "") { delete groupMap; }
+
+ if (m->control_pressed) { remove(outputFileName.c_str()); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
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