+++ /dev/null
-//
-// getcoremicrobiomcommand.cpp
-// Mothur
-//
-// Created by John Westcott on 5/8/12.
-// Copyright (c) 2012 Schloss Lab. All rights reserved.
-//
-
-#include "getcoremicrobiomcommand.h"
-
-
-//**********************************************************************************************************************
-vector<string> GetCoreMicroBiomCommand::setParameters(){
- try {
- CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-
- //every command must have inputdir and outputdir. This allows mothur users to redirect input and output files.
- 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, "GetCoreMicroBiomCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string GetCoreMicroBiomCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The new command allows you to ....\n";
- helpString += "The new command parameters are: ....\n";
- helpString += "The whatever parameter is used to ....\n";
- helpString += "The new command should be in the following format: \n";
- helpString += "new(...)\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "GetCoreMicroBiomCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-GetCoreMicroBiomCommand::GetCoreMicroBiomCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["coremicrobiom"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "GetCoreMicroBiomCommand", "GetCoreMicroBiomCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-GetCoreMicroBiomCommand::GetCoreMicroBiomCommand(string option) {
- try {
- abort = false; calledHelp = false; allLines = 1;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- //valid paramters for this command
- 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; }
- }
-
-
- //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("relabund");
- //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["relabund"] = inputDir + it->second; }
- }
-
- it = parameters.find("shared");
- //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["shared"] = inputDir + it->second; }
- }
- }
-
-
- //check for parameters
- sharedfile = validParameter.validFile(parameters, "shared", true);
- if (sharedfile == "not open") { abort = true; }
- else if (sharedfile == "not found") { sharedfile = ""; }
- else { inputFileName = sharedfile; format = "sharedfile"; m->setSharedFile(sharedfile); }
-
- relabundfile = validParameter.validFile(parameters, "relabund", true);
- if (relabundfile == "not open") { abort = true; }
- else if (relabundfile == "not found") { relabundfile = ""; }
- else { inputFileName = relabundfile; format = "relabund"; m->setRelAbundFile(relabundfile); }
-
- if ((relabundfile == "") && (sharedfile == "")) {
- //is there are current file available for either of these?
- //give priority to shared, then relabund
- sharedfile = m->getSharedFile();
- if (sharedfile != "") { inputFileName = sharedfile; format="sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
- else {
- relabundfile = m->getRelAbundFile();
- if (relabundfile != "") { inputFileName = relabundfile; format="relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
- else {
- m->mothurOut("No valid current files. You must provide a shared or relabund."); m->mothurOutEndLine();
- abort = true;
- }
- }
- }
-
- //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(inputFileName); //if user entered a file with a path then preserve it
- }
-
- string groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; }
- else { m->splitAtDash(groups, Groups); }
- m->setGroups(Groups);
-
- string label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; }
- else {
- if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetCoreMicroBiomCommand", "GetCoreMicroBiomCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int GetCoreMicroBiomCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- InputData input(inputFileName, format);
- vector<SharedRAbundFloatVector*> lookup = input.getSharedRAbundFloatVectors();
- string lastLabel = lookup[0]->getLabel();
-
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-
- createTable(lookup);
-
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
- }
-
- if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = lookup[0]->getLabel();
-
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- lookup = input.getSharedRAbundFloatVectors(lastLabel);
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-
- createTable(lookup);
-
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
-
- //restore real lastlabel to save below
- lookup[0]->setLabel(saveLabel);
- }
-
- lastLabel = lookup[0]->getLabel();
- //prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- //get next line to process
- lookup = input.getSharedRAbundFloatVectors();
- }
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
- lookup = input.getSharedRAbundFloatVectors(lastLabel);
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-
- createTable(lookup);
-
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- }
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- //output files created by command
- 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, "GetCoreMicroBiomCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int GetCoreMicroBiomCommand::createTable(vector<SharedRAbundFloatVector*>& lookup){
- try {
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiom";
- outputNames.push_back(outputFileName); outputTypes["coremicrobiom"].push_back(outputFileName);
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- int numSamples = lookup.size();
- int numOtus = lookup[0]->getNumBins();
-
- //table is 100 by numsamples
- //question we are answering is: what fraction of OTUs in a study have a relative abundance at or above %X
- //in at least %Y samples. x goes from 0 to 100, y from 1 to numSamples
- vector< vector<double> > table; table.resize(101);
- for (int i = 0; i < table.size(); i++) { table[i].resize(numSamples, 0.0); }
-
- for (int i = 0; i < numOtus; i++) {
-
- if (m->control_pressed) { break; }
-
- //count number of samples in this otu with a relabund >= spot in count
- vector<int> counts; counts.resize(101, 0);
-
- for (int j = 0; j < lookup.size(); j++) {
- double relabund = lookup[j]->getAbundance(i);
- int wholeRelabund = (int) (floor(relabund*100));
- for (int k = 0; k < wholeRelabund+1; k++) { counts[k]++; }
- }
-
- //add this otus info to table
- for (int j = 0; j < table.size(); j++) {
- for (int k = 0; k < counts[j]; k++) { table[j][k]++; }
- }
- }
-
- //format output
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
- out << "NumSamples\t";
-
- //convert table counts to percents
- for (int i = 0; i < table.size(); i++) {
- out << "Relabund-" << i << "%\t";
- if (m->control_pressed) { break; }
- for (int j = 0; j < table[i].size(); j++) { table[i][j] /= (double) numOtus; }
- }
- out << endl;
-
- for (int i = 0; i < numSamples; i++) {
- if (m->control_pressed) { break; }
- out << i+1 << '\t';
- for (int j = 0; j < table.size(); j++) { out << table[j][i] << '\t'; }
- out << endl;
- }
-
- out.close();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "GetCoreMicroBiomCommand", "createTable");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-
projects / mothur.git / commitdiff