+++ /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 .seq.count 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; }
- }else { m->setNameFile(namefile); }
-
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { abort = true; }
- else if (groupfile == "not found") { groupfile = ""; }
- else { m->setGroupFile(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)) + "seq.count";
- m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName);
- out << "Representative_Sequence\ttotal\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();
- vector<string> nameGroups = groupMap->getNamesOfGroups();
- util->setGroups(Groups, nameGroups);
- 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);
-
- int total = 0;
- 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;
- }
-
- total += names.size();
- }
- in.close();
-
- if (groupfile != "") { delete groupMap; }
-
- if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
-
- m->mothurOutEndLine();
- m->mothurOut("Total number of sequences: " + toString(total)); m->mothurOutEndLine();
- 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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