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/*
* secondarystructurecommand.cpp
* Mothur
*
* Created by westcott on 9/18/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "secondarystructurecommand.h"
#include "sequence.hpp"
#include "counttable.h"
//**********************************************************************************************************************
vector<string> AlignCheckCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","aligncheck",false,true,true); parameters.push_back(pfasta);
CommandParameter pmap("map", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pmap);
CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pcount);
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, "AlignCheckCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string AlignCheckCommand::getHelpString(){
try {
string helpString = "";
helpString += "The align.check command reads a fasta file and map file as well as an optional name or count file.\n";
helpString += "It outputs a file containing the secondary structure matches in the .align.check file.\n";
helpString += "The align.check command parameters are fasta and map, both are required.\n";
helpString += "The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n";
helpString += "Example align.check(map=silva.ss.map, fasta=amazon.fasta).\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, "AlignCheckCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string AlignCheckCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "aligncheck") { pattern = "[filename],align.check"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "AlignCheckCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
AlignCheckCommand::AlignCheckCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["aligncheck"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
exit(1);
}
}
//**********************************************************************************************************************
AlignCheckCommand::AlignCheckCommand(string option) {
try {
abort = false; calledHelp = false;
haderror = 0;
//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["aligncheck"] = 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("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("map");
//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["map"] = 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; }
}
it = parameters.find("count");
//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["count"] = inputDir + it->second; }
}
}
//check for required parameters
mapfile = validParameter.validFile(parameters, "map", true);
if (mapfile == "not open") { abort = true; }
else if (mapfile == "not found") { mapfile = ""; m->mothurOut("You must provide an map file."); m->mothurOutEndLine(); abort = true; }
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { fastafile = ""; 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); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { abort = true; countfile = ""; }
else if (countfile == "not found") { countfile = ""; }
else { m->setCountTableFile(countfile); }
if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); 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 = "";
outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
if (countfile == "") {
if ((namefile == "") && (fastafile != "")){
vector<string> files; files.push_back(fastafile);
parser.getNameFile(files);
}
}
}
}
catch(exception& e) {
m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
exit(1);
}
}
//**********************************************************************************************************************
int AlignCheckCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get secondary structure info.
readMap();
if (namefile != "") { nameMap = m->readNames(namefile); }
else if (countfile != "") {
CountTable ct;
ct.readTable(countfile, false, false);
nameMap = ct.getNameMap();
}
if (m->control_pressed) { return 0; }
ifstream in;
m->openInputFile(fastafile, in);
ofstream out;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
string outfile = getOutputFileName("aligncheck",variables);
m->openOutputFile(outfile, out);
out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t';
out << "loop" << '\t' << "tilde" << '\t' << "total" << '\t' << "numseqs" << endl;
vector<int> pound;
vector<int> dash;
vector<int> plus;
vector<int> equal;
vector<int> loop;
vector<int> tilde;
vector<int> total;
int count = 0;
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outfile); return 0; }
Sequence seq(in); m->gobble(in);
if (seq.getName() != "") {
statData data = getStats(seq.getAligned());
if (haderror == 1) { m->control_pressed = true; break; }
int num = 1;
if ((namefile != "") || (countfile != "")) {
//make sure this sequence is in the namefile, else error
map<string, int>::iterator it = nameMap.find(seq.getName());
if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + seq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
else { num = it->second; }
}
//for each sequence this sequence represents
for (int i = 0; i < num; i++) {
pound.push_back(data.pound);
dash.push_back(data.dash);
plus.push_back(data.plus);
equal.push_back(data.equal);
loop.push_back(data.loop);
tilde.push_back(data.tilde);
total.push_back(data.total);
}
count++;
out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
out << data.loop << '\t' << data.tilde << '\t' << data.total << '\t' << num << endl;
}
}
in.close();
out.close();
if (m->control_pressed) { m->mothurRemove(outfile); return 0; }
sort(pound.begin(), pound.end());
sort(dash.begin(), dash.end());
sort(plus.begin(), plus.end());
sort(equal.begin(), equal.end());
sort(loop.begin(), loop.end());
sort(tilde.begin(), tilde.end());
sort(total.begin(), total.end());
int size = pound.size();
int ptile0_25 = int(size * 0.025);
int ptile25 = int(size * 0.250);
int ptile50 = int(size * 0.500);
int ptile75 = int(size * 0.750);
int ptile97_5 = int(size * 0.975);
int ptile100 = size - 1;
if (m->control_pressed) { m->mothurRemove(outfile); return 0; }
m->mothurOutEndLine();
m->mothurOut("\t\tPound\tDash\tPlus\tEqual\tLoop\tTilde\tTotal"); m->mothurOutEndLine();
m->mothurOut("Minimum:\t" + toString(pound[0]) + "\t" + toString(dash[0]) + "\t" + toString(plus[0]) + "\t" + toString(equal[0]) + "\t" + toString(loop[0]) + "\t" + toString(tilde[0]) + "\t" + toString(total[0])); m->mothurOutEndLine();
m->mothurOut("2.5%-tile:\t" + toString(pound[ptile0_25]) + "\t" + toString(dash[ptile0_25]) + "\t" + toString(plus[ptile0_25]) + "\t" + toString(equal[ptile0_25]) + "\t"+ toString(loop[ptile0_25]) + "\t"+ toString(tilde[ptile0_25]) + "\t"+ toString(total[ptile0_25])); m->mothurOutEndLine();
m->mothurOut("25%-tile:\t" + toString(pound[ptile25]) + "\t" + toString(dash[ptile25]) + "\t" + toString(plus[ptile25]) + "\t" + toString(equal[ptile25]) + "\t" + toString(loop[ptile25]) + "\t" + toString(tilde[ptile25]) + "\t" + toString(total[ptile25])); m->mothurOutEndLine();
m->mothurOut("Median: \t" + toString(pound[ptile50]) + "\t" + toString(dash[ptile50]) + "\t" + toString(plus[ptile50]) + "\t" + toString(equal[ptile50]) + "\t" + toString(loop[ptile50]) + "\t" + toString(tilde[ptile50]) + "\t" + toString(total[ptile50])); m->mothurOutEndLine();
m->mothurOut("75%-tile:\t" + toString(pound[ptile75]) + "\t" + toString(dash[ptile75]) + "\t" + toString(plus[ptile75]) + "\t" + toString(equal[ptile75]) + "\t" + toString(loop[ptile75]) + "\t" + toString(tilde[ptile75]) + "\t" + toString(total[ptile75])); m->mothurOutEndLine();
m->mothurOut("97.5%-tile:\t" + toString(pound[ptile97_5]) + "\t" + toString(dash[ptile97_5]) + "\t" + toString(plus[ptile97_5]) + "\t" + toString(equal[ptile97_5]) + "\t" + toString(loop[ptile97_5]) + "\t" + toString(tilde[ptile97_5]) + "\t" + toString(total[ptile97_5])); m->mothurOutEndLine();
m->mothurOut("Maximum:\t" + toString(pound[ptile100]) + "\t" + toString(dash[ptile100]) + "\t" + toString(plus[ptile100]) + "\t" + toString(equal[ptile100]) + "\t" + toString(loop[ptile100]) + "\t" + toString(tilde[ptile100]) + "\t" + toString(total[ptile100])); m->mothurOutEndLine();
if ((namefile == "") && (countfile == "")) { m->mothurOut("# of Seqs:\t" + toString(count)); m->mothurOutEndLine(); }
else { m->mothurOut("# of unique seqs:\t" + toString(count)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(size)); m->mothurOutEndLine(); }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outfile); m->mothurOutEndLine(); outputNames.push_back(outfile); outputTypes["aligncheck"].push_back(outfile);
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "AlignCheckCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
void AlignCheckCommand::readMap(){
try {
structMap.resize(1, 0);
ifstream in;
m->openInputFile(mapfile, in);
while(!in.eof()){
int position;
in >> position;
structMap.push_back(position);
m->gobble(in);
}
in.close();
seqLength = structMap.size();
//check you make sure is structMap[10] = 380 then structMap[380] = 10.
for(int i=0;i<seqLength;i++){
if(structMap[i] != 0){
if(structMap[structMap[i]] != i){
m->mothurOut("Your map file contains an error: line " + toString(i) + " does not match line " + toString(structMap[i]) + "."); m->mothurOutEndLine();
}
}
}
}
catch(exception& e) {
m->errorOut(e, "AlignCheckCommand", "readMap");
exit(1);
}
}
/**************************************************************************************************/
statData AlignCheckCommand::getStats(string sequence){
try {
statData data;
sequence = "*" + sequence; // need to pad the sequence so we can index it by 1
int length = sequence.length();
if (length != seqLength) { m->mothurOut("your sequences are " + toString(length) + " long, but your map file only contains " + toString(seqLength) + " entries. please correct."); m->mothurOutEndLine(); haderror = 1; return data; }
for(int i=1;i<length;i++){
if(structMap[i] != 0){
if(sequence[i] == 'A'){
if(sequence[structMap[i]] == 'T') { data.tilde++; }
else if(sequence[structMap[i]] == 'A') { data.pound++; }
else if(sequence[structMap[i]] == 'G') { data.equal++; }
else if(sequence[structMap[i]] == 'C') { data.pound++; }
else if(sequence[structMap[i]] == '-') { data.pound++; }
data.total++;
}
else if(sequence[i] == 'T'){
if(sequence[structMap[i]] == 'T') { data.plus++; }
else if(sequence[structMap[i]] == 'A') { data.tilde++; }
else if(sequence[structMap[i]] == 'G') { data.dash++; }
else if(sequence[structMap[i]] == 'C') { data.pound++; }
else if(sequence[structMap[i]] == '-') { data.pound++; }
data.total++;
}
else if(sequence[i] == 'G'){
if(sequence[structMap[i]] == 'T') { data.dash++; }
else if(sequence[structMap[i]] == 'A') { data.equal++; }
else if(sequence[structMap[i]] == 'G') { data.pound++; }
else if(sequence[structMap[i]] == 'C') { data.tilde++; }
else if(sequence[structMap[i]] == '-') { data.pound++; }
data.total++;
}
else if(sequence[i] == 'C'){
if(sequence[structMap[i]] == 'T') { data.pound++; }
else if(sequence[structMap[i]] == 'A') { data.pound++; }
else if(sequence[structMap[i]] == 'G') { data.tilde++; }
else if(sequence[structMap[i]] == 'C') { data.pound++; }
else if(sequence[structMap[i]] == '-') { data.pound++; }
data.total++;
}
else if(sequence[i] == '-'){
if(sequence[structMap[i]] == 'T') { data.pound++; data.total++; }
else if(sequence[structMap[i]] == 'A') { data.pound++; data.total++; }
else if(sequence[structMap[i]] == 'G') { data.pound++; data.total++; }
else if(sequence[structMap[i]] == 'C') { data.pound++; data.total++; }
else if(sequence[structMap[i]] == '-') { /*donothing*/ }
}
}
else if(isalnum(sequence[i])){
data.loop++;
data.total++;
}
}
return data;
}
catch(exception& e) {
m->errorOut(e, "AlignCheckCommand", "getStats");
exit(1);
}
}
//**********************************************************************************************************************
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