//**********************************************************************************************************************
vector<string> AlignCheckCommand::getValidParameters(){
try {
- string Array[] = {"fasta","map", "outputdir","inputdir"};
+ string Array[] = {"fasta", "name","map", "outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
return myArray;
}
else {
//valid paramters for this command
- string Array[] = {"fasta","map", "outputdir","inputdir"};
+ string Array[] = {"fasta","name","map", "outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
//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
if (fastafile == "not open") { abort = true; }
else if (fastafile == "not found") { fastafile = ""; m->mothurOut("You must provide an fasta file."); m->mothurOutEndLine(); abort = true; }
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { 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 = "";
//get secondary structure info.
readMap();
+ if (namefile != "") { nameMap = m->readNames(namefile); }
+
+ if (m->control_pressed) { return 0; }
+
ifstream in;
m->openInputFile(fastafile, in);
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" << 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 (seq.getName() != "") {
statData data = getStats(seq.getAligned());
- if (haderror == 1) { break; }
+ 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()) { cout << "[ERROR]: " << seq.getName() << " is not in your namefile, please correct." << endl; 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;
}
}
if (m->control_pressed) { remove(outfile.c_str()); 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) { remove(outfile.c_str()); 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);
exit(1);
}
}
-
-
//**********************************************************************************************************************
projects / mothur.git / blobdiff