+++ /dev/null
-/*
- * splitgroupscommand.cpp
- * Mothur
- *
- * Created by westcott on 9/20/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "splitgroupscommand.h"
-#include "sharedutilities.h"
-#include "sequenceparser.h"
-
-//**********************************************************************************************************************
-vector<string> SplitGroupCommand::setParameters(){
- try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); 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, "SplitGroupCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string SplitGroupCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The split.group command reads a group file, and parses your fasta and names files by groups. \n";
- helpString += "The split.group command parameters are fasta, name, group and groups.\n";
- helpString += "The fasta and group parameters are required.\n";
- helpString += "The groups parameter allows you to select groups to create files for. \n";
- helpString += "For example if you set groups=A-B-C, you will get a .A.fasta, .A.names, .B.fasta, .B.names, .C.fasta, .C.names files. \n";
- helpString += "If you want .fasta and .names files for all groups, set groups=all. \n";
- helpString += "The split.group command should be used in the following format: split.group(fasta=yourFasta, group=yourGroupFile).\n";
- helpString += "Example: split.group(fasta=abrecovery.fasta, group=abrecovery.groups).\n";
- helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "SplitGroupCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-SplitGroupCommand::SplitGroupCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "SplitGroupCommand", "SplitGroupCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-SplitGroupCommand::SplitGroupCommand(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 (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["name"] = 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("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; }
- }
-
- it = parameters.find("fasta");
- //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["fasta"] = inputDir + it->second; }
- }
-
- 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; }
- }
-
- }
-
-
- namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { namefile = ""; abort = true; }
- else if (namefile == "not found") { namefile = ""; }
- else { m->setNameFile(namefile); }
-
- fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") {
- fastafile = m->getFastaFile();
- if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setFastaFile(fastafile); }
-
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { groupfile = ""; abort = true; }
- else if (groupfile == "not found") {
- groupfile = m->getGroupFile();
- if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setGroupFile(groupfile); }
-
- groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; }
- else { 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(groupfile); }
-
- if (namefile == "") {
- vector<string> files; files.push_back(fastafile);
- parser.getNameFile(files);
- }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "SplitGroupCommand", "SplitAbundCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int SplitGroupCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- SequenceParser* parser;
-
- if (namefile == "") { parser = new SequenceParser(groupfile, fastafile); }
- else { parser = new SequenceParser(groupfile, fastafile, namefile); }
-
- if (m->control_pressed) { delete parser; return 0; }
-
- vector<string> namesGroups = parser->getNamesOfGroups();
- SharedUtil util; util.setGroups(Groups, namesGroups);
-
- string fastafileRoot = outputDir + m->getRootName(m->getSimpleName(fastafile));
- string namefileRoot = outputDir + m->getRootName(m->getSimpleName(namefile));
-
- m->mothurOutEndLine();
- for (int i = 0; i < Groups.size(); i++) {
-
- m->mothurOut("Processing group: " + Groups[i]); m->mothurOutEndLine();
-
- string newFasta = fastafileRoot + Groups[i] + ".fasta";
- string newName = namefileRoot + Groups[i] + ".names";
-
- parser->getSeqs(Groups[i], newFasta, false);
- outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta);
- if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- if (namefile != "") {
- parser->getNameMap(Groups[i], newName);
- outputNames.push_back(newName); outputTypes["name"].push_back(newName);
- }
-
- if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
- }
-
- delete parser;
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- string current = "";
- itTypes = outputTypes.find("fasta");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
- }
-
- itTypes = outputTypes.find("name");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
- }
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
- m->mothurOutEndLine();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SplitGroupCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-
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