vector<string> ConsensusSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ 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 plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
CommandParameter pcutoff("cutoff", "Number", "", "100", "", "", "",false,false); parameters.push_back(pcutoff);
try {
string helpString = "";
helpString += "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";
- helpString += "The consensus.seqs command parameters are fasta, list, name, cutoff and label.\n";
+ helpString += "The consensus.seqs command parameters are fasta, list, name, count, cutoff and label.\n";
helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required, unless you have a valid current fasta file. \n";
helpString += "The list parameter allows you to enter a your list file. \n";
helpString += "The name parameter allows you to enter a names file associated with the fasta file. \n";
else {
if (type == "fasta") { outputFileName = "cons.fasta"; }
else if (type == "name") { outputFileName = "cons.names"; }
+ else if (type == "count") { outputFileName = "cons.count.table"; }
else if (type == "summary") { outputFileName = "cons.summary"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
}
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
outputTypes["summary"] = tempOutNames;
}
catch(exception& e) {
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
outputTypes["summary"] = tempOutNames;
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["list"] = 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; }
+ }
}
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; }
+
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
else if (listfile == "not found") { listfile = ""; }
//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 = m->hasPath(fastafile); }
- if (namefile == ""){
- vector<string> files; files.push_back(fastafile);
- parser.getNameFile(files);
- }
+ if (countfile == "") {
+ if (namefile == ""){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
}
}
catch(exception& e) {
if (m->control_pressed) { return 0; }
if (namefile != "") { readNames(); }
+ if (countfile != "") { ct.readTable(countfile); }
if (m->control_pressed) { return 0; }
string outputFastaFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("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++) {
-
- if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- 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; }
-
- }
-
+
vector< vector<float> > percentages; percentages.resize(5);
for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
string consSeq = "";
+ int thisCount;
//get counts
for (int j = 0; j < seqLength; j++) {
vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
int numDots = 0;
-
- for (int i = 0; i < seqs.size(); i++) {
+ thisCount = 0;
+ for (map<string, string>::iterator it = fastaMap.begin(); it != fastaMap.end(); it++) {
- 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]++; }
+ string thisSeq = it->second;
+ int size = 0;
+
+ if (countfile != "") { size = ct.getNumSeqs(it->first); }
+ else {
+ map<string, int>::iterator itCount = nameFileMap.find(it->first);
+ if (itCount != nameFileMap.end()) {
+ size = itCount->second;
+ }else { m->mothurOut("[ERROR]: file mismatch, aborting.\n"); m->control_pressed = true; break; }
+ }
+
+ for (int k = 0; k < size; k++) {
+ if (thisSeq[j] == '.') { numDots++; }
+
+ char base = toupper(thisSeq[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]++; }
+ thisCount++;
+ }
}
char conBase = '.';
- if (numDots != seqs.size()) { conBase = getBase(counts, seqs.size()); }
+ if (numDots != thisCount) { conBase = getBase(counts, thisCount); }
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();
-
+ percentages[0][j] = counts[0] / (float) thisCount;
+ percentages[1][j] = counts[1] / (float) thisCount;
+ percentages[2][j] = counts[2] / (float) thisCount;
+ percentages[3][j] = counts[3] / (float) thisCount;
+ percentages[4][j] = counts[4] / (float) thisCount;
}
for (int j = 0; j < seqLength; j++) {
- outSummary << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << seqs.size() << '\t' << consSeq[j] << endl;
+ outSummary << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << thisCount << '\t' << consSeq[j] << endl;
}
outFasta << ">conseq" << endl << consSeq << endl;
outSummary.close(); outFasta.close();
-
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}else {
if (m->control_pressed) { outSummary.close(); outName.close(); outFasta.close(); return 0; }
string bin = list->get(i);
-
- string newName = "";
- string consSeq = getConsSeq(bin, outSummary, newName, i);
+ string consSeq = getConsSeq(bin, outSummary, i);
outFasta << ">seq" << (i+1) << endl << consSeq << endl;
- outName << "seq" << (i+1) << '\t' << "seq" << (i+1) << "," << newName << endl;
+ outName << "seq" << (i+1) << '\t' << "seq" << (i+1) << "," << bin << endl;
}
outSummary.close(); outName.close(); outFasta.close();
}
//***************************************************************************************************************
-//made this smart enough to owrk with unique or non unique list file
-string ConsensusSeqsCommand::getConsSeq(string bin, ofstream& outSummary, string& name, int binNumber){
+string ConsensusSeqsCommand::getConsSeq(string bin, ofstream& outSummary, int binNumber){
try{
string consSeq = "";
bool error = false;
-
- //the whole bin is the second column if no names file, otherwise build it
- name = bin;
- if (namefile != "") { name = ""; }
-
+ int totalSize=0;
+
vector<string> binNames;
m->splitAtComma(bin, binNames);
-
- //get sequence strings for each name in the bin
- vector<string> seqs;
-
- set<string> addedAlready;
- int seqLength = 0;
- for (int i = 0; i < binNames.size(); i++) {
-
- map<string, string>::iterator it;
-
- it = nameMap.find(binNames[i]);
- if (it == nameMap.end()) {
- if (namefile == "") { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta file, please correct."); m->mothurOutEndLine(); error = true; }
- else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta or name file, please correct."); m->mothurOutEndLine(); error = true; }
- break;
- }else {
-
- //add sequence string to seqs vector to process below
- 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(); error = true; break; }
-
- if (namefile != "") {
- //did we add this line from name file already?
- if (addedAlready.count(it->second) == 0) {
- name += "," + nameFileMap[it->second];
- addedAlready.insert(it->second);
- }
- }
-
- }
- }
-
- if (error) { m->control_pressed = true; return consSeq; }
-
- if (namefile != "") { name = name.substr(1); }
-
- vector< vector<float> > percentages; percentages.resize(5);
+
+ vector< vector<float> > percentages; percentages.resize(5);
for (int j = 0; j < percentages.size(); j++) { percentages[j].resize(seqLength, 0.0); }
-
- //get counts
- for (int j = 0; j < seqLength; j++) {
-
- if (m->control_pressed) { return consSeq; }
-
- vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
- int numDots = 0;
-
- 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, seqs.size()); }
-
- 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();
-
+
+ if (countfile != "") {
+ //get counts
+ for (int j = 0; j < seqLength; j++) {
+
+ if (m->control_pressed) { return consSeq; }
+
+ vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
+ int numDots = 0;
+ totalSize = 0;
+ for (int i = 0; i < binNames.size(); i++) {
+ if (m->control_pressed) { return consSeq; }
+
+ string thisSeq = "";
+ map<string, string>::iterator itFasta = fastaMap.find(binNames[i]);
+ if (itFasta != fastaMap.end()) {
+ thisSeq = itFasta->second;
+ }else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta file, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ int size = ct.getNumSeqs(binNames[i]);
+ if (size != 0) {
+ for (int k = 0; k < size; k++) {
+ if (thisSeq[j] == '.') { numDots++; }
+
+ char base = toupper(thisSeq[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]++; }
+ totalSize++;
+ }
+ }else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your count file, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ }
+ char conBase = '.';
+ if (numDots != totalSize) { conBase = getBase(counts, totalSize); }
+
+ consSeq += conBase;
+
+ percentages[0][j] = counts[0] / (float) totalSize;
+ percentages[1][j] = counts[1] / (float) totalSize;
+ percentages[2][j] = counts[2] / (float) totalSize;
+ percentages[3][j] = counts[3] / (float) totalSize;
+ percentages[4][j] = counts[4] / (float) totalSize;
+ }
+
+ }else {
+
+ //get sequence strings for each name in the bin
+ vector<string> seqs;
+ for (int i = 0; i < binNames.size(); i++) {
+
+ map<string, string>::iterator it;
+ it = nameMap.find(binNames[i]);
+ if (it == nameMap.end()) {
+ if (namefile == "") { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta file, please correct."); m->mothurOutEndLine(); error = true; }
+ else { m->mothurOut("[ERROR]: " + binNames[i] + " is not in your fasta or name file, please correct."); m->mothurOutEndLine(); error = true; }
+ break;
+ }else {
+ //add sequence string to seqs vector to process below
+ map<string, string>::iterator itFasta = fastaMap.find(it->second);
+
+ if (itFasta != fastaMap.end()) {
+ string seq = itFasta->second;
+ seqs.push_back(seq);
+ }else { m->mothurOut("[ERROR]: file mismatch, aborting. \n"); }
+ }
+ }
+
+ if (error) { m->control_pressed = true; return consSeq; }
+ totalSize = seqs.size();
+ //get counts
+ for (int j = 0; j < seqLength; j++) {
+
+ if (m->control_pressed) { return consSeq; }
+
+ vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
+ int numDots = 0;
+
+ 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, seqs.size()); }
+
+ 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();
+
+ }
}
-
+
+
+
for (int j = 0; j < seqLength; j++) {
- outSummary << (binNumber + 1) << '\t' << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << seqs.size() << '\t' << consSeq[j] << endl;
+ outSummary << (binNumber + 1) << '\t' << (j+1) << '\t' << percentages[0][j] << '\t'<< percentages[1][j] << '\t'<< percentages[2][j] << '\t' << percentages[3][j] << '\t' << percentages[4][j] << '\t' << totalSize << '\t' << consSeq[j] << endl;
}
return consSeq;
ifstream in;
m->openInputFile(fastafile, in);
-
+ seqLength = 0;
+
while (!in.eof()) {
if (m->control_pressed) { break; }
if (name != "") {
fastaMap[name] = seq.getAligned();
nameMap[name] = name; //set nameMap incase no names file
- nameFileMap[name] = name;
+ nameFileMap[name] = 1;
+
+ if (seqLength == 0) { seqLength = seq.getAligned().length(); }
+ else if (seqLength != seq.getAligned().length()) { m->mothurOut("[ERROR]: sequence are not the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true; break; }
}
}
it = nameMap.find(thisname);
if (it != nameMap.end()) { //then this sequence was in the fastafile
- nameFileMap[thisname] = repnames; //for later when outputting the new namesFile if the list file is unique
+ nameFileMap[thisname] = m->getNumNames(repnames); //for later when outputting the new namesFile if the list file is unique
vector<string> splitRepNames;
m->splitAtComma(repnames, splitRepNames);
projects / mothur.git / blobdiff