listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
- else if (listfile == "not found") { listfile = ""; m->mothurOut("list is a required parameter for the consensus.seqs command."); m->mothurOutEndLine(); abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
void ConsensusSeqsCommand::help(){
try {
- m->mothurOut("The consensus.seqs command reads a fastafile and listfile and creates a consensus sequence for each otu. Sequences must be aligned.\n");
+ m->mothurOut("The consensus.seqs command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.\n");
m->mothurOut("The consensus.seqs command parameters are fasta, list, name and label.\n");
m->mothurOut("The fasta parameter allows you to enter the fasta file containing your sequences, and is required. \n");
m->mothurOut("The list parameter allows you to enter a your list file. \n");
if (m->control_pressed) { return 0; }
- InputData* input = new InputData(listfile, "list");
- ListVector* list = input->getListVector();
-
- string lastLabel = list->getLabel();
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete list; delete input; return 0; }
-
- if(allLines == 1 || labels.count(list->getLabel()) == 1){
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ if (listfile == "") {
+
+ ofstream outSummary;
+ string outputSummaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.summary";
+ m->openOutputFile(outputSummaryFile, outSummary);
+ outSummary.setf(ios::fixed, ios::floatfield); outSummary.setf(ios::showpoint);
+ outputNames.push_back(outputSummaryFile); outputTypes["summary"].push_back(outputSummaryFile);
+
+ ofstream outFasta;
+ string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "cons.fasta";
+ m->openOutputFile(outputFastaFile, outFasta);
+ outputNames.push_back(outputFastaFile); outputTypes["fasta"].push_back(outputFastaFile);
+
+ vector<string> seqs;
+ int seqLength = 0;
+ for (map<string, string>::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
- processList(list);
+ if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
+ string seq = fastaMap[it->second];
+ seqs.push_back(seq);
+
+ if (seqLength == 0) { seqLength = seq.length(); }
+ else if (seqLength != seq.length()) { m->mothurOut("[ERROR]: sequence are not the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+
}
- if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = list->getLabel();
+ vector< vector<float> > percentages; percentages.resize(5);
+ for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
+
+ string consSeq = "";
+ //get counts
+ for (int j = 0; j < seqLength; j++) {
- delete list;
+ if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
- list = input->getListVector(lastLabel);
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
+ int numDots = 0;
- processList(list);
+ for (int i = 0; i < seqs.size(); i++) {
+
+ if (seqs[i][j] == '.') { numDots++; }
+
+ char base = toupper(seqs[i][j]);
+ if (base == 'A') { counts[0]++; }
+ else if (base == 'T') { counts[1]++; }
+ else if (base == 'G') { counts[2]++; }
+ else if (base == 'C') { counts[3]++; }
+ else { counts[4]++; }
+ }
+
+ char conBase = '.';
+ if (numDots != seqs.size()) { conBase = getBase(counts); }
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
+ consSeq += conBase;
+
+ percentages[0][j] = counts[0] / (float) seqs.size();
+ percentages[1][j] = counts[1] / (float) seqs.size();
+ percentages[2][j] = counts[2] / (float) seqs.size();
+ percentages[3][j] = counts[3] / (float) seqs.size();
+ percentages[4][j] = counts[4] / (float) seqs.size();
- //restore real lastlabel to save below
- list->setLabel(saveLabel);
}
- lastLabel = list->getLabel();
+ outSummary << "A" << '\t';
+ for (int j = 0; j < seqLength; j++) { outSummary << percentages[0][j] << '\t'; }
+ outSummary << endl;
+ outSummary << "T" << '\t';
+ for (int j = 0; j < seqLength; j++) { outSummary << percentages[1][j] << '\t'; }
+ outSummary << endl;
+ outSummary << "G" << '\t';
+ for (int j = 0; j < seqLength; j++) { outSummary << percentages[2][j] << '\t'; }
+ outSummary << endl;
+ outSummary << "C" << '\t';
+ for (int j = 0; j < seqLength; j++) { outSummary << percentages[3][j] << '\t'; }
+ outSummary << endl;
+ outSummary << "Gap" << '\t';
+ for (int j = 0; j < seqLength; j++) { outSummary << percentages[4][j] << '\t'; }
+ outSummary << endl;
- delete list; list = NULL;
+
+ outFasta << ">conseq" << endl << consSeq << endl;
+
+ outSummary.close(); outFasta.close();
- //get next line to process
- list = input->getListVector();
- }
-
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } if (list != NULL) { delete list; } delete input; return 0; }
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }else {
+
+
+ InputData* input = new InputData(listfile, "list");
+ ListVector* list = input->getListVector();
+
+ string lastLabel = list->getLabel();
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete list; delete input; return 0; }
+
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ processList(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+
+ list = input->getListVector(lastLabel);
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ processList(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
+
+ lastLabel = list->getLabel();
+
+ delete list; list = NULL;
+
+ //get next line to process
+ list = input->getListVector();
}
- }
-
- //run last label if you need to
- if (needToRun == true) {
- if (list != NULL) { delete list; }
- list = input->getListVector(lastLabel);
- m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } if (list != NULL) { delete list; } delete input; return 0; }
- processList(list);
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
- delete list; list = NULL;
+ //run last label if you need to
+ if (needToRun == true) {
+ if (list != NULL) { delete list; }
+
+ list = input->getListVector(lastLabel);
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ processList(list);
+
+ delete list; list = NULL;
+ }
+
+ if (list != NULL) { delete list; }
+ delete input;
}
- if (list != NULL) { delete list; }
- delete input;
-
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
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