2 * secondarystructurecommand.cpp
5 * Created by westcott on 9/18/09.
6 * Copyright 2009 Schloss Lab. All rights reserved.
10 #include "secondarystructurecommand.h"
11 #include "sequence.hpp"
13 //**********************************************************************************************************************
14 vector<string> AlignCheckCommand::setParameters(){
16 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
17 CommandParameter pmap("map", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pmap);
18 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
19 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
20 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
22 vector<string> myArray;
23 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
27 m->errorOut(e, "AlignCheckCommand", "setParameters");
31 //**********************************************************************************************************************
32 string AlignCheckCommand::getHelpString(){
34 string helpString = "";
35 helpString += "The align.check command reads a fasta file and map file as well as an optional name file.\n";
36 helpString += "It outputs a file containing the secondary structure matches in the .align.check file.\n";
37 helpString += "The align.check command parameters are fasta and map, both are required.\n";
38 helpString += "The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n";
39 helpString += "Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n";
40 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
44 m->errorOut(e, "AlignCheckCommand", "getHelpString");
48 //**********************************************************************************************************************
49 string AlignCheckCommand::getOutputFileNameTag(string type, string inputName=""){
51 string outputFileName = "";
52 map<string, vector<string> >::iterator it;
54 //is this a type this command creates
55 it = outputTypes.find(type);
56 if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
58 if (type == "aligncheck") { outputFileName = "align.check"; }
59 else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
61 return outputFileName;
64 m->errorOut(e, "AlignCheckCommand", "getOutputFileNameTag");
68 //**********************************************************************************************************************
69 AlignCheckCommand::AlignCheckCommand(){
71 abort = true; calledHelp = true;
73 vector<string> tempOutNames;
74 outputTypes["aligncheck"] = tempOutNames;
77 m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
81 //**********************************************************************************************************************
83 AlignCheckCommand::AlignCheckCommand(string option) {
85 abort = false; calledHelp = false;
88 //allow user to run help
89 if(option == "help") { help(); abort = true; calledHelp = true; }
90 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
93 vector<string> myArray = setParameters();
95 OptionParser parser(option);
96 map<string,string> parameters = parser.getParameters();
98 ValidParameters validParameter;
99 map<string,string>::iterator it;
101 //check to make sure all parameters are valid for command
102 for (it = parameters.begin(); it != parameters.end(); it++) {
103 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
106 //initialize outputTypes
107 vector<string> tempOutNames;
108 outputTypes["aligncheck"] = tempOutNames;
110 //if the user changes the input directory command factory will send this info to us in the output parameter
111 string inputDir = validParameter.validFile(parameters, "inputdir", false);
112 if (inputDir == "not found"){ inputDir = ""; }
115 it = parameters.find("fasta");
116 //user has given a template file
117 if(it != parameters.end()){
118 path = m->hasPath(it->second);
119 //if the user has not given a path then, add inputdir. else leave path alone.
120 if (path == "") { parameters["fasta"] = inputDir + it->second; }
123 it = parameters.find("map");
124 //user has given a template file
125 if(it != parameters.end()){
126 path = m->hasPath(it->second);
127 //if the user has not given a path then, add inputdir. else leave path alone.
128 if (path == "") { parameters["map"] = inputDir + it->second; }
131 it = parameters.find("name");
132 //user has given a template file
133 if(it != parameters.end()){
134 path = m->hasPath(it->second);
135 //if the user has not given a path then, add inputdir. else leave path alone.
136 if (path == "") { parameters["name"] = inputDir + it->second; }
140 //check for required parameters
141 mapfile = validParameter.validFile(parameters, "map", true);
142 if (mapfile == "not open") { abort = true; }
143 else if (mapfile == "not found") { mapfile = ""; m->mothurOut("You must provide an map file."); m->mothurOutEndLine(); abort = true; }
145 fastafile = validParameter.validFile(parameters, "fasta", true);
146 if (fastafile == "not open") { fastafile = ""; abort = true; }
147 else if (fastafile == "not found") {
148 fastafile = m->getFastaFile();
149 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
150 else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
151 }else { m->setFastaFile(fastafile); }
153 namefile = validParameter.validFile(parameters, "name", true);
154 if (namefile == "not open") { namefile = ""; abort = true; }
155 else if (namefile == "not found") { namefile = ""; }
156 else { m->setNameFile(namefile); }
158 //if the user changes the output directory command factory will send this info to us in the output parameter
159 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
161 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
164 if ((namefile == "") && (fastafile != "")){
165 vector<string> files; files.push_back(fastafile);
166 parser.getNameFile(files);
171 catch(exception& e) {
172 m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
176 //**********************************************************************************************************************
178 int AlignCheckCommand::execute(){
181 if (abort == true) { if (calledHelp) { return 0; } return 2; }
183 //get secondary structure info.
186 if (namefile != "") { nameMap = m->readNames(namefile); }
188 if (m->control_pressed) { return 0; }
191 m->openInputFile(fastafile, in);
194 string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("aligncheck");
195 m->openOutputFile(outfile, out);
198 out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t';
199 out << "loop" << '\t' << "tilde" << '\t' << "total" << '\t' << "numseqs" << endl;
211 if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outfile); return 0; }
213 Sequence seq(in); m->gobble(in);
214 if (seq.getName() != "") {
215 statData data = getStats(seq.getAligned());
217 if (haderror == 1) { m->control_pressed = true; break; }
220 if (namefile != "") {
221 //make sure this sequence is in the namefile, else error
222 map<string, int>::iterator it = nameMap.find(seq.getName());
224 if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + seq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
225 else { num = it->second; }
228 //for each sequence this sequence represents
229 for (int i = 0; i < num; i++) {
230 pound.push_back(data.pound);
231 dash.push_back(data.dash);
232 plus.push_back(data.plus);
233 equal.push_back(data.equal);
234 loop.push_back(data.loop);
235 tilde.push_back(data.tilde);
236 total.push_back(data.total);
240 out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
241 out << data.loop << '\t' << data.tilde << '\t' << data.total << '\t' << num << endl;
248 if (m->control_pressed) { m->mothurRemove(outfile); return 0; }
250 sort(pound.begin(), pound.end());
251 sort(dash.begin(), dash.end());
252 sort(plus.begin(), plus.end());
253 sort(equal.begin(), equal.end());
254 sort(loop.begin(), loop.end());
255 sort(tilde.begin(), tilde.end());
256 sort(total.begin(), total.end());
257 int size = pound.size();
259 int ptile0_25 = int(size * 0.025);
260 int ptile25 = int(size * 0.250);
261 int ptile50 = int(size * 0.500);
262 int ptile75 = int(size * 0.750);
263 int ptile97_5 = int(size * 0.975);
264 int ptile100 = size - 1;
266 if (m->control_pressed) { m->mothurRemove(outfile); return 0; }
268 m->mothurOutEndLine();
269 m->mothurOut("\t\tPound\tDash\tPlus\tEqual\tLoop\tTilde\tTotal"); m->mothurOutEndLine();
270 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();
271 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();
272 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();
273 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();
274 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();
275 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();
276 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();
277 if (namefile == "") { m->mothurOut("# of Seqs:\t" + toString(count)); m->mothurOutEndLine(); }
278 else { m->mothurOut("# of unique seqs:\t" + toString(count)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(size)); m->mothurOutEndLine(); }
281 m->mothurOutEndLine();
282 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
283 m->mothurOut(outfile); m->mothurOutEndLine(); outputNames.push_back(outfile); outputTypes["aligncheck"].push_back(outfile);
284 m->mothurOutEndLine();
289 catch(exception& e) {
290 m->errorOut(e, "AlignCheckCommand", "execute");
294 //**********************************************************************************************************************
295 void AlignCheckCommand::readMap(){
298 structMap.resize(1, 0);
301 m->openInputFile(mapfile, in);
306 structMap.push_back(position);
311 seqLength = structMap.size();
314 //check you make sure is structMap[10] = 380 then structMap[380] = 10.
315 for(int i=0;i<seqLength;i++){
316 if(structMap[i] != 0){
317 if(structMap[structMap[i]] != i){
318 m->mothurOut("Your map file contains an error: line " + toString(i) + " does not match line " + toString(structMap[i]) + "."); m->mothurOutEndLine();
325 catch(exception& e) {
326 m->errorOut(e, "AlignCheckCommand", "readMap");
330 /**************************************************************************************************/
332 statData AlignCheckCommand::getStats(string sequence){
336 sequence = "*" + sequence; // need to pad the sequence so we can index it by 1
338 int length = sequence.length();
340 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; }
342 for(int i=1;i<length;i++){
343 if(structMap[i] != 0){
344 if(sequence[i] == 'A'){
345 if(sequence[structMap[i]] == 'T') { data.tilde++; }
346 else if(sequence[structMap[i]] == 'A') { data.pound++; }
347 else if(sequence[structMap[i]] == 'G') { data.equal++; }
348 else if(sequence[structMap[i]] == 'C') { data.pound++; }
349 else if(sequence[structMap[i]] == '-') { data.pound++; }
352 else if(sequence[i] == 'T'){
353 if(sequence[structMap[i]] == 'T') { data.plus++; }
354 else if(sequence[structMap[i]] == 'A') { data.tilde++; }
355 else if(sequence[structMap[i]] == 'G') { data.dash++; }
356 else if(sequence[structMap[i]] == 'C') { data.pound++; }
357 else if(sequence[structMap[i]] == '-') { data.pound++; }
360 else if(sequence[i] == 'G'){
361 if(sequence[structMap[i]] == 'T') { data.dash++; }
362 else if(sequence[structMap[i]] == 'A') { data.equal++; }
363 else if(sequence[structMap[i]] == 'G') { data.pound++; }
364 else if(sequence[structMap[i]] == 'C') { data.tilde++; }
365 else if(sequence[structMap[i]] == '-') { data.pound++; }
368 else if(sequence[i] == 'C'){
369 if(sequence[structMap[i]] == 'T') { data.pound++; }
370 else if(sequence[structMap[i]] == 'A') { data.pound++; }
371 else if(sequence[structMap[i]] == 'G') { data.tilde++; }
372 else if(sequence[structMap[i]] == 'C') { data.pound++; }
373 else if(sequence[structMap[i]] == '-') { data.pound++; }
376 else if(sequence[i] == '-'){
377 if(sequence[structMap[i]] == 'T') { data.pound++; data.total++; }
378 else if(sequence[structMap[i]] == 'A') { data.pound++; data.total++; }
379 else if(sequence[structMap[i]] == 'G') { data.pound++; data.total++; }
380 else if(sequence[structMap[i]] == 'C') { data.pound++; data.total++; }
381 else if(sequence[structMap[i]] == '-') { /*donothing*/ }
384 else if(isalnum(sequence[i])){
392 catch(exception& e) {
393 m->errorOut(e, "AlignCheckCommand", "getStats");
397 //**********************************************************************************************************************