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);
}
ifstream in;
- int ableToOpen = openInputFile(filenames[i], in);
+ int ableToOpen = openInputFile(filenames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + getSimpleName(filenames[i]);
+ m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ableToOpen = openInputFile(tryPath, in, "noerror");
+ filenames[i] = tryPath;
+ }
+ }
in.close();
if (ableToOpen == 1) {
- m->mothurOut(filenames[i] + " will be disregarded."); m->mothurOutEndLine();
+ m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
filenames.erase(filenames.begin()+i);
i--;
//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, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + getSimpleName(accnosFileNames[i]);
+ m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ableToOpen = openInputFile(tryPath, in, "noerror");
+ accnosFileNames[i] = tryPath;
+ }
+ }
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + accnosFileNames[i] + ". It 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) {
void SffInfoCommand::help(){
try {
- m->mothurOut("The sffinfo command reads a sff file and outputs a .sff.txt file.\n");
-
- m->mothurOut("Example sffinfo(sff=...).\n");
+ m->mothurOut("The sffinfo command reads a sff file and extracts the sequence data.\n");
+ m->mothurOut("The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, and trim. sff is required. \n");
+ m->mothurOut("The sff parameter allows you to enter the sff file you would like to extract data from. You may enter multiple files by separating them by -'s.\n");
+ m->mothurOut("The fasta parameter allows you to indicate if you would like a fasta formatted file generated. Default=True. \n");
+ m->mothurOut("The qfile parameter allows you to indicate if you would like a quality file generated. Default=True. \n");
+ m->mothurOut("The flow parameter allows you to indicate if you would like a flowgram file generated. Default=False. \n");
+ m->mothurOut("The sfftxt parameter allows you to indicate if you would like a sff.txt file generated. Default=False. \n");
+ m->mothurOut("The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values. Default=True. \n");
+ m->mothurOut("The accnos parameter allows you to provide a accnos file containing the names of the sequences you would like extracted. You may enter multiple files by separating them by -'s. \n");
+ m->mothurOut("Example sffinfo(sff=mySffFile.sff, trim=F).\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n\n");
}
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; } }
- count++;
+ //print
+ if (print) {
+ if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read, readheader); }
+ if (fasta) { printFastaSeqData(outFasta, read, readheader); }
+ if (qual) { printQualSeqData(outQual, read, readheader); }
+ if (flow) { printFlowSeqData(outFlow, read, readheader); }
+ }
+ count++;
+
//report progress
- if((count+1) % 500 == 0){ m->mothurOut(toString(count+1)); m->mothurOutEndLine(); }
+ if((count+1) % 10000 == 0){ m->mothurOut(toString(count+1)); m->mothurOutEndLine(); }
if (m->control_pressed) { count = 0; break; }
}
//report progress
- if (!m->control_pressed) { if((count) % 500 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } }
+ if (!m->control_pressed) { if((count) % 10000 != 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;
}
try {
if (!in.eof()) {
-
+
//read magic number
- char buffer[sizeof(header.magicNumber)];
- in.read(buffer, sizeof(header.magicNumber));
+ char buffer[4];
+ in.read(buffer, 4);
header.magicNumber = be_int4(*(unsigned int *)(&buffer));
-
+
//read version
char buffer9[4];
in.read(buffer9, 4);
for (int i = 0; i < 4; i++) { header.version += toString((int)(buffer9[i])); }
//read offset
- char buffer2 [sizeof(header.indexOffset)];
- in.read(buffer2, sizeof(header.indexOffset));
+ char buffer2 [8];
+ in.read(buffer2, 8);
header.indexOffset = be_int8(*(unsigned long int *)(&buffer2));
//read index length
- char buffer3 [sizeof(header.indexLength)];
- in.read(buffer3, sizeof(header.indexLength));
+ char buffer3 [4];
+ in.read(buffer3, 4);
header.indexLength = be_int4(*(unsigned int *)(&buffer3));
//read num reads
- char buffer4 [sizeof(header.numReads)];
- in.read(buffer4, sizeof(header.numReads));
+ char buffer4 [4];
+ in.read(buffer4, 4);
header.numReads = be_int4(*(unsigned int *)(&buffer4));
//read header length
- char buffer5 [sizeof(header.headerLength)];
- in.read(buffer5, sizeof(header.headerLength));
+ char buffer5 [2];
+ in.read(buffer5, 2);
header.headerLength = be_int2(*(unsigned short *)(&buffer5));
//read key length
- char buffer6 [sizeof(header.keyLength)];
- in.read(buffer6, sizeof(header.keyLength));
+ char buffer6 [2];
+ in.read(buffer6, 2);
header.keyLength = be_int2(*(unsigned short *)(&buffer6));
//read number of flow reads
- char buffer7 [sizeof(header.numFlowsPerRead)];
- in.read(buffer7, sizeof(header.numFlowsPerRead));
+ char buffer7 [2];
+ in.read(buffer7, 2);
header.numFlowsPerRead = be_int2(*(unsigned short *)(&buffer7));
//read format code
header.flogramFormatCode = (int)(buffer8[0]);
//read flow chars
- char tempBuffer [header.numFlowsPerRead];
- in.read(tempBuffer, header.numFlowsPerRead);
+ char* tempBuffer = new char[header.numFlowsPerRead];
+ in.read(&(*tempBuffer), header.numFlowsPerRead);
header.flowChars = tempBuffer;
if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead); }
+ delete[] tempBuffer;
//read key
- char tempBuffer2 [header.keyLength];
- in.read(tempBuffer2, header.keyLength);
+ char* tempBuffer2 = new char[header.keyLength];
+ in.read(&(*tempBuffer2), header.keyLength);
header.keySequence = tempBuffer2;
if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength); }
+ delete[] tempBuffer2;
/* Pad to 8 chars */
- int spotInFile = in.tellg();
- int spot = (spotInFile + 7)& ~7; // ~ inverts
+ unsigned long int spotInFile = in.tellg();
+ unsigned long int spot = (spotInFile + 7)& ~7; // ~ inverts
in.seekg(spot);
}else{
if (!in.eof()) {
//read header length
- char buffer [sizeof(header.headerLength)];
- in.read(buffer, sizeof(header.headerLength));
+ char buffer [2];
+ in.read(buffer, 2);
header.headerLength = be_int2(*(unsigned short *)(&buffer));
//read name length
- char buffer2 [sizeof(header.nameLength)];
- in.read(buffer2, sizeof(header.nameLength));
+ char buffer2 [2];
+ in.read(buffer2, 2);
header.nameLength = be_int2(*(unsigned short *)(&buffer2));
//read num bases
- char buffer3 [sizeof(header.numBases)];
- in.read(buffer3, sizeof(header.numBases));
+ char buffer3 [4];
+ in.read(buffer3, 4);
header.numBases = be_int4(*(unsigned int *)(&buffer3));
//read clip qual left
- char buffer4 [sizeof(header.clipQualLeft)];
- in.read(buffer4, sizeof(header.clipQualLeft));
+ char buffer4 [2];
+ in.read(buffer4, 2);
header.clipQualLeft = be_int2(*(unsigned short *)(&buffer4));
+ header.clipQualLeft = 5;
//read clip qual right
- char buffer5 [sizeof(header.clipQualRight)];
- in.read(buffer5, sizeof(header.clipQualRight));
+ char buffer5 [2];
+ in.read(buffer5, 2);
header.clipQualRight = be_int2(*(unsigned short *)(&buffer5));
//read clipAdapterLeft
- char buffer6 [sizeof(header.clipAdapterLeft)];
- in.read(buffer6, sizeof(header.clipAdapterLeft));
+ char buffer6 [2];
+ in.read(buffer6, 2);
header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
//read clipAdapterRight
- char buffer7 [sizeof(header.clipAdapterRight)];
- in.read(buffer7, sizeof(header.clipAdapterRight));
+ char buffer7 [2];
+ in.read(buffer7, 2);
header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
//read name
- char tempBuffer [header.nameLength];
- in.read(tempBuffer, header.nameLength);
+ char* tempBuffer = new char[header.nameLength];
+ in.read(&(*tempBuffer), header.nameLength);
header.name = tempBuffer;
if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength); }
+ delete[] tempBuffer;
/* Pad to 8 chars */
- int spotInFile = in.tellg();
- int spot = (spotInFile + 7)& ~7;
+ unsigned long int spotInFile = in.tellg();
+ unsigned long int spot = (spotInFile + 7)& ~7;
in.seekg(spot);
}else{
//read flowgram
read.flowgram.resize(numFlowReads);
for (int i = 0; i < numFlowReads; i++) {
- char buffer [sizeof(unsigned short)];
- in.read(buffer, (sizeof(unsigned short)));
+ char buffer [2];
+ in.read(buffer, 2);
read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
}
in.read(temp, 1);
read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
}
-
+
//read bases
- char tempBuffer[numBases];
- in.read(tempBuffer, numBases);
+ char* tempBuffer = new char[numBases];
+ in.read(&(*tempBuffer), numBases);
read.bases = tempBuffer;
if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases); }
+ delete[] tempBuffer;
- //read flowgram
+ //read qual scores
read.qualScores.resize(numBases);
for (int i = 0; i < numBases; i++) {
char temp[1];
in.read(temp, 1);
read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
}
-
+
/* Pad to 8 chars */
- int spotInFile = in.tellg();
- int spot = (spotInFile + 7)& ~7;
+ unsigned long int spotInFile = in.tellg();
+ unsigned long int spot = (spotInFile + 7)& ~7;
in.seekg(spot);
}else{
//**********************************************************************************************************************
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, Header& header) {
try {
- out << "FlowGram: ";
+ out << "Flowgram: ";
for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t'; }
out << endl << "Flow Indexes: ";
int sum = 0;
for (int i = 0; i < read.flowIndex.size(); i++) { sum += read.flowIndex[i]; out << sum << '\t'; }
+ //make the bases you want to clip lowercase and the bases you want to keep upper case
+ for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
+ for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { read.bases[i] = toupper(read.bases[i]); }
+ for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) { read.bases[i] = tolower(read.bases[i]); }
+
out << endl << "Bases: " << read.bases << endl << "Quality Scores: ";
for (int i = 0; i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
+
+
out << endl << endl;
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) {
+ if(header.clipQualRight != 0){
+ seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
+ }
+ else {
+ seq = seq.substr(header.clipQualLeft-1);
+ }
+ }else{
+ //if you wanted the sfftxt then you already converted the bases to the right case
+ if (!sfftxt) {
+ //make the bases you want to clip lowercase and the bases you want to keep upper case
+ if(header.clipQualRight == 0){ header.clipQualRight = seq.length(); }
+ for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]); }
+ for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { seq[i] = toupper(seq[i]); }
+ for (int i = (header.clipQualRight-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
+ }
+ }
+
+ 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) {
+ if(header.clipQualRight != 0){
+ out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
+ for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { out << read.qualScores[i] << '\t'; }
+ }
+ else{
+ out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
+ for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); 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 / blobdiff