SffInfoCommand::SffInfoCommand(string option) {
try {
abort = false;
+ hasAccnos = false;
//allow user to run help
if(option == "help") { help(); abort = true; }
else {
//valid paramters for this command
- string Array[] = {"sff","outputdir","inputdir", "outputdir"};
+ string Array[] = {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
//make sure there is at least one valid file left
if (filenames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
}
+
+ accnosName = validParameter.validFile(parameters, "accnos", false);
+ if (accnosName == "not found") { accnosName = ""; }
+ else {
+ hasAccnos = true;
+ splitAtDash(accnosName, accnosFileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < accnosFileNames.size(); i++) {
+ if (inputDir != "") {
+ string path = hasPath(accnosFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { accnosFileNames[i] = inputDir + accnosFileNames[i]; }
+ }
+
+ ifstream in;
+ int ableToOpen = openInputFile(accnosFileNames[i], in);
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut(accnosFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ accnosFileNames.erase(accnosFileNames.begin()+i);
+ i--;
+ }
+ }
+
+ //make sure there is at least one valid file left
+ if (accnosFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ if (hasAccnos) {
+ if (accnosFileNames.size() != filenames.size()) { abort = true; m->mothurOut("If you provide a accnos file, you must have one for each sff file."); m->mothurOutEndLine(); }
+ }
+
+ string temp = validParameter.validFile(parameters, "qfile", false); if (temp == "not found"){ temp = "T"; }
+ qual = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "fasta", false); if (temp == "not found"){ temp = "T"; }
+ fasta = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "flow", false); if (temp == "not found"){ temp = "F"; }
+ flow = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found"){ temp = "T"; }
+ trim = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "sfftxt", false); if (temp == "not found"){ temp = "F"; }
+ sfftxt = isTrue(temp);
}
}
catch(exception& e) {
m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
- if (outputDir == "") { outputDir += hasPath(filenames[s]); }
- string outputFileName = outputDir + getRootName(getSimpleName(filenames[s])) + "sff.txt";
-
- int numReads = extractSffInfo(filenames[s], outputFileName);
+ string accnos = "";
+ if (hasAccnos) { accnos = accnosFileNames[s]; }
- outputNames.push_back(outputFileName);
+ int numReads = extractSffInfo(filenames[s], accnos);
m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
}
}
}
//**********************************************************************************************************************
-int SffInfoCommand::extractSffInfo(string input, string output){
+int SffInfoCommand::extractSffInfo(string input, string accnos){
try {
- ofstream out;
- openOutputFile(output, out);
+ if (outputDir == "") { outputDir += hasPath(input); }
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ if (accnos != "") { readAccnosFile(accnos); }
+ else { seqNames.clear(); }
+
+ ofstream outSfftxt, outFasta, outQual, outFlow;
+ string outFastaFileName, outQualFileName;
+ string sfftxtFileName = outputDir + getRootName(getSimpleName(input)) + "sff.txt";
+ string outFlowFileName = outputDir + getRootName(getSimpleName(input)) + "flow";
+ if (trim) {
+ outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "fasta";
+ outQualFileName = outputDir + getRootName(getSimpleName(input)) + "qual";
+ }else{
+ outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "raw.fasta";
+ outQualFileName = outputDir + getRootName(getSimpleName(input)) + "raw.qual";
+ }
+
+ if (sfftxt) { openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint); outputNames.push_back(sfftxtFileName); }
+ if (fasta) { openOutputFile(outFastaFileName, outFasta); outputNames.push_back(outFastaFileName); }
+ if (qual) { openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); }
+ if (flow) { openOutputFile(outFlowFileName, outFlow); outputNames.push_back(outFlowFileName); }
ifstream in;
in.open(input.c_str(), ios::binary);
CommonHeader header;
readCommonHeader(in, header);
- //print common header
- printCommonHeader(out, header);
-
int count = 0;
//check magic number and version
if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
+
+ //print common header
+ if (sfftxt) { printCommonHeader(outSfftxt, header); }
//read through the sff file
while (!in.eof()) {
+ bool print = true;
+
//read header
Header readheader;
readHeader(in, readheader);
-
- //print header
- printHeader(out, readheader);
//read data
seqRead read;
readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
-
- //print data
- printSeqData(out, read);
+
+ //if you have provided an accosfile and this seq is not in it, then dont print
+ if (seqNames.size() != 0) { if (seqNames.count(readheader.name) == 0) { print = false; } }
+
+ //print
+ if (print) {
+ if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read); }
+ if (fasta) { printFastaSeqData(outFasta, read, readheader); }
+ if (qual) { printQualSeqData(outQual, read, readheader); }
+ if (flow) { printFlowSeqData(outFlow, read, readheader); }
+ }
count++;
if (!m->control_pressed) { if((count) % 500 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } }
in.close();
- out.close();
+
+ if (sfftxt) { outSfftxt.close(); }
+ if (fasta) { outFasta.close(); }
+ if (qual) { outQual.close(); }
+ if (flow) { outFlow.close(); }
return count;
}
//**********************************************************************************************************************
int SffInfoCommand::printHeader(ofstream& out, Header& header) {
try {
+
out << ">" << header.name << endl;
out << "Run Prefix: " << endl;
out << "Region #: " << endl;
}
//**********************************************************************************************************************
-int SffInfoCommand::printSeqData(ofstream& out, seqRead& read) {
+int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read) {
try {
out << "FlowGram: ";
return 0;
}
catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "printSeqData");
+ m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
+ try {
+
+ string seq = read.bases;
+
+
+ if (trim) {
+ seq = seq.substr(header.clipQualLeft, (header.clipQualRight-header.clipQualLeft));
+ }
+
+ out << ">" << header.name << endl;
+ out << seq << endl;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
+ try {
+
+ if (trim) {
+ out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
+ for (int i = header.clipQualLeft; i < (header.clipQualRight-header.clipQualLeft); i++) { out << read.qualScores[i] << '\t'; }
+ }else{
+ out << ">" << header.name << " length=" << read.qualScores.size() << endl;
+ for (int i = 0; i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
+ }
+
+ out << endl;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "printQualSeqData");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
+ try {
+
+ out << ">" << header.name << endl;
+ for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t'; }
+ out << endl;
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SffInfoCommand::readAccnosFile(string filename) {
+ try {
+ //remove old names
+ seqNames.clear();
+
+ ifstream in;
+ openInputFile(filename, in);
+ string name;
+
+ while(!in.eof()){
+ in >> name; gobble(in);
+
+ seqNames.insert(name);
+
+ if (m->control_pressed) { seqNames.clear(); break; }
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "readAccnosFile");
exit(1);
}
}
projects / mothur.git / commitdiff