+++ /dev/null
-/*
- * secondarystructurecommand.cpp
- * Mothur
- *
- * Created by westcott on 9/18/09.
- * Copyright 2009 Schloss Lab. All rights reserved.
- *
- */
-
-#include "secondarystructurecommand.h"
-#include "sequence.hpp"
-
-//**********************************************************************************************************************
-vector<string> AlignCheckCommand::setParameters(){
- try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pmap("map", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pmap);
- 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.\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);
- }
-}
-//**********************************************************************************************************************
-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; }
- }
- }
-
- //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); }
-
- //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 ((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); }
-
- if (m->control_pressed) { return 0; }
-
- ifstream in;
- m->openInputFile(fastafile, in);
-
- ofstream out;
- string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check";
- 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 != "") {
- //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 == "") { 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 Name: "); 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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