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/*
* makegroupcommand.cpp
* Mothur
*
* Created by westcott on 5/7/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "makegroupcommand.h"
#include "sequence.hpp"
#include "counttable.h"
#include "filefile.hpp"
//**********************************************************************************************************************
vector<string> MakeGroupCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "none","count",false,true,true); parameters.push_back(pfasta);
CommandParameter pfile("file", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "none","count",false,false,true); parameters.push_back(pfile);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pgroups);
CommandParameter poutput("output", "String", "", "", "", "", "","",false,false); parameters.push_back(poutput);
CommandParameter pformat("format", "Multiple", "count-group", "count", "", "", "","",false,false,true); parameters.push_back(pformat);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["count"] = tempOutNames;
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, "MakeGroupCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string MakeGroupCommand::getHelpString(){
try {
string helpString = "";
helpString += "The make.count (also called make.group) command will create a count or group file.\nThe make.count command reads a file file, fasta file or series of fasta files and creates a group file or count file.\n";
helpString += "The make.group command parameters are file, fasta, groups, format and output. File or Fasta and groups are required.\n";
helpString += "The output parameter allows you to specify the name of group file or count file created. \n";
helpString += "The format parameter allows you to specify whether the outputtted file is a group file or count file. Default=count. \n";
helpString += "The make.count command should be in the following format: \n";
helpString += "make.count(file=yourFileFile). \n";
helpString += "make.count(fasta=yourFastaFiles, groups=yourGroups). \n";
helpString += "Example make.count(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string MakeGroupCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "group") { pattern = "[filename],groups"; }
else if (type == "count") { pattern = "[filename],count_table"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
MakeGroupCommand::MakeGroupCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validPath(parameters, "inputdir");
if (inputDir == "not found"){ inputDir = ""; }
fileFile = validParameter.validFile(parameters, "file");
if (fileFile == "not open") { abort = true; }
else if (fileFile == "not found") { fileFile = ""; }
fastaFileNames = validParameter.validFiles(parameters, "fasta");
if (fastaFileNames.size() != 0) {
if (fastaFileNames[0] == "not open") { abort = true; }
else { current->setFastaFile(fastaFileNames[0]); }
}
//make sure there is at least one valid file left
if ((fileFile == "") && (fastaFileNames.size() == 0)) { m->mothurOut("[ERROR]: no valid files. Please provide a file file or fasta file.\n"); abort = true; }
output = validParameter.validPath(parameters, "output");
if (output == "not found") { output = ""; }
format = validParameter.valid(parameters, "format"); if (format == "not found"){ format = "count"; }
if ((format != "count") && (format != "group")) { m->mothurOut("\n[WARNING]: invalid format option: choices are count or group, using count.\n"); format="count"; }
groups = validParameter.valid(parameters, "groups");
if (groups == "not found") {
if (fileFile == "") {
m->mothurOut("[ERROR]: The groups parameter is required unless you are using a file file.\n"); abort = true;
}
}
else { util.splitAtDash(groups, groupsNames); }
if ((fileFile == "") && (groupsNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: You do not have the same number of valid fastfile files as groups. This could be because we could not open a fastafile.\n"); abort = true; }
}
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
exit(1);
}
}
//**********************************************************************************************************************
int MakeGroupCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
string outputFileRoot = "";
map<string, string> seqGroup;
map<string, long long> groupCounts;
if (fileFile == "") {
processFastaFiles(seqGroup, groupCounts);
//if no output filename given, create root
if (output == "") {
if (outputdir == "") { outputdir = util.hasPath(fastaFileNames[0]); }
outputFileRoot = outputdir + util.getRootName(util.getSimpleName(fastaFileNames[0]));
if (fastaFileNames.size() > 1) { outputFileRoot = outputdir + "merge."; }
}
}else {
processFileFile(seqGroup, groupCounts);
if (output == "") {
if (outputdir == "") { outputdir = util.hasPath(fileFile); }
outputFileRoot = outputdir + util.getRootName(util.getSimpleName(fileFile));
}
}
if (m->getControl_pressed()) { return 0; }
//if user provided output filename, then use it
string outputFileName = util.getFullPathName(output);
if (output == "") {
map<string, string> variables;
variables["[filename]"] = outputFileRoot;
outputFileName = getOutputFileName(format,variables);
outputNames.push_back(outputFileName); outputTypes[format].push_back(outputFileName);
}
if (format == "count") {
CountTable ct; ct.createTable(seqGroup);
ct.printCompressedTable(outputFileName);
}else{
ofstream out; util.openOutputFile(outputFileName, out);
for (map<string, string>::iterator it = seqGroup.begin(); it != seqGroup.end(); it++) {
out << it->first << '\t' << it->second << endl;
}
out.close();
}
long long total = 0;
if (groupCounts.size() != 0) { m->mothurOut("\nGroup count: \n"); }
for (map<string, long long>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) { total += it->second; m->mothurOut(it->first + "\t" + toString(it->second) + "\n"); }
if (total != 0) { m->mothurOut("\nTotal of all groups is " + toString(total) + "\n"); }
m->mothurOut("\nOutput File Names: " + outputFileName + "\n\n");
//set group file as new current groupfile
string currentName = "";
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setGroupFile(currentName); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setCountFile(currentName); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
void MakeGroupCommand::processFastaFiles(map<string, string>& seqGroup, map<string, long long>& groupCounts){
try {
util.checkGroupNames(groupsNames);
for (int i = 0; i < fastaFileNames.size(); i++) {
if (m->getControl_pressed()) { break; }
m->mothurOutJustToScreen("\nAssigning sequences from file " + fastaFileNames[i] + " to group " + groupsNames[i] + ":\t");
ifstream in; util.openInputFile(fastaFileNames[i], in);
long long count = 0;
while (!in.eof()) {
if (m->getControl_pressed()) { break; }
Sequence seq(in); gobble(in);
if (seq.getName() != "") { seqGroup[seq.getName()] = groupsNames[i]; count++; }
}
in.close();
m->mothurOutJustToScreen(toString(count) + " sequences assigned to group " + groupsNames[i] + "\n");
groupCounts[groupsNames[i]] = count;
}
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "processFastaFiles");
exit(1);
}
}
//**********************************************************************************************************************
void MakeGroupCommand::processFileFile(map<string, string>& seqGroup, map<string, long long>& groupCounts){
try {
FileFile dataFile(fileFile, "make.count");
vector< vector<string> > files = dataFile.getFiles();
groupsNames = dataFile.getGroupNames();
int fileOption = dataFile.getFileFormat(); //7: group -> fastaFile, 8: group -> fowardFasta,reverseFasta
if (fileOption == 7) {
for (auto thisVector : files) {
for (auto file : thisVector) {
fastaFileNames.push_back(file);
}
}
}else {
for (auto thisVector : files) {
if (thisVector.size() > 0) { fastaFileNames.push_back(thisVector[0]); }
}
}
processFastaFiles(seqGroup, groupCounts);
}
catch(exception& e) {
m->errorOut(e, "MakeGroupCommand", "processFileFile");
exit(1);
}
}
//**********************************************************************************************************************
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