#include "secondarystructurecommand.h"
#include "sequence.hpp"
+#include "counttable.h"
//**********************************************************************************************************************
-vector<string> AlignCheckCommand::getValidParameters(){
+vector<string> AlignCheckCommand::setParameters(){
try {
- string Array[] = {"fasta","map", "outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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", "getValidParameters");
+ m->errorOut(e, "AlignCheckCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-AlignCheckCommand::AlignCheckCommand(){
+string AlignCheckCommand::getHelpString(){
try {
- abort = true;
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["aligncheck"] = tempOutNames;
+ 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", "AlignCheckCommand");
+ m->errorOut(e, "AlignCheckCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> AlignCheckCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta","map"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCheckCommand", "getRequiredParameters");
- 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);
+ }
}
//**********************************************************************************************************************
-vector<string> AlignCheckCommand::getRequiredFiles(){
+AlignCheckCommand::AlignCheckCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["aligncheck"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "AlignCheckCommand", "getRequiredFiles");
+ m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
exit(1);
}
}
AlignCheckCommand::AlignCheckCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
haderror = 0;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta","map", "outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//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
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") { abort = true; }
- else if (fastafile == "not found") { fastafile = ""; m->mothurOut("You must provide an fasta file."); m->mothurOutEndLine(); abort = 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", "RemoveSeqsCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-void AlignCheckCommand::help(){
- try {
- m->mothurOut("The align.check command reads a fasta file and map file.\n");
- m->mothurOut("It outputs a file containing the secondary structure matches in the .align.check file.\n");
- m->mothurOut("The align.check command parameters are fasta and map, both are required.\n");
- m->mothurOut("The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n");
- m->mothurOut("Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCheckCommand", "help");
+ m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
exit(1);
}
}
-
//**********************************************************************************************************************
int AlignCheckCommand::execute(){
try {
- if (abort == true) { return 0; }
+ 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);
+ nameMap = ct.getNameMap();
+ }
+
+ if (m->control_pressed) { return 0; }
+
ifstream in;
m->openInputFile(fastafile, in);
ofstream out;
- string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check";
+ 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" << endl;
+ 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(); remove(outfile.c_str()); return 0; }
+ 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) { break; }
+ 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 << endl;
+ out << data.loop << '\t' << data.tilde << '\t' << data.total << '\t' << num << endl;
}
}
in.close();
out.close();
- if (m->control_pressed) { remove(outfile.c_str()); return 0; }
+ 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("Output File Name: "); 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();
exit(1);
}
}
-
-
//**********************************************************************************************************************
projects / mothur.git / blobdiff