#include "sffinfocommand.h"
#include "endiannessmacros.h"
+//**********************************************************************************************************************
+vector<string> SffInfoCommand::getValidParameters(){
+ try {
+ string Array[] = {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SffInfoCommand::SffInfoCommand(){
+ try {
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["flow"] = tempOutNames;
+ outputTypes["sfftxt"] = tempOutNames;
+ outputTypes["qual"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SffInfoCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"sff"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SffInfoCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffInfoCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
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);
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["flow"] = tempOutNames;
+ outputTypes["sfftxt"] = tempOutNames;
+ outputTypes["qual"] = tempOutNames;
+
//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 = ""; }
sffFilename = validParameter.validFile(parameters, "sff", false);
if (sffFilename == "not found") { m->mothurOut("sff is a required parameter for the sffinfo command."); m->mothurOutEndLine(); abort = true; }
else {
- splitAtDash(sffFilename, filenames);
+ m->splitAtDash(sffFilename, filenames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < filenames.size(); i++) {
if (inputDir != "") {
- string path = hasPath(filenames[i]);
+ string path = m->hasPath(filenames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { filenames[i] = inputDir + filenames[i]; }
}
ifstream in;
- int ableToOpen = openInputFile(filenames[i], in);
+ int ableToOpen = m->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() + m->getSimpleName(filenames[i]);
+ m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ filenames[i] = tryPath;
+ }
+ }
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(filenames[i]);
+ m->mothurOut("Unable to open " + filenames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ 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;
+ m->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 = m->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 = m->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() + m->getSimpleName(accnosFileNames[i]);
+ m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ accnosFileNames[i] = tryPath;
+ }
+ }
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(accnosFileNames[i]);
+ m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ 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 = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "fasta", false); if (temp == "not found"){ temp = "T"; }
+ fasta = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "flow", false); if (temp == "not found"){ temp = "F"; }
+ flow = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found"){ temp = "T"; }
+ trim = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "sfftxt", false); if (temp == "not found"){ temp = "F"; }
+ sfftxt = m->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) {
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ int start = time(NULL);
+
m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
- if (outputDir == "") { outputDir += hasPath(filenames[s]); }
- string outputFileName = outputDir + getRootName(getSimpleName(filenames[s])) + "sff.txt";
-
- extractSffInfo(filenames[s], outputFileName);
+ string accnos = "";
+ if (hasAccnos) { accnos = accnosFileNames[s]; }
- outputNames.push_back(outputFileName);
+ int numReads = extractSffInfo(filenames[s], accnos);
- m->mothurOut("Done."); m->mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
}
}
//**********************************************************************************************************************
-int SffInfoCommand::extractSffInfo(string input, string output){
+int SffInfoCommand::extractSffInfo(string input, string accnos){
try {
- ofstream out;
- openOutputFile(output, out);
+
+ if (outputDir == "") { outputDir += m->hasPath(input); }
+
+ if (accnos != "") { readAccnosFile(accnos); }
+ else { seqNames.clear(); }
+
+ ofstream outSfftxt, outFasta, outQual, outFlow;
+ string outFastaFileName, outQualFileName;
+ string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
+ string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
+ if (trim) {
+ outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "fasta";
+ outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "qual";
+ }else{
+ outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.fasta";
+ outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.qual";
+ }
+
+ if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint); outputNames.push_back(sfftxtFileName); outputTypes["sfftxt"].push_back(sfftxtFileName); }
+ if (fasta) { m->openOutputFile(outFastaFileName, outFasta); outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
+ if (qual) { m->openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); outputTypes["qual"].push_back(outQualFileName); }
+ if (flow) { m->openOutputFile(outFlowFileName, outFlow); outputNames.push_back(outFlowFileName); outputTypes["flow"].push_back(outFlowFileName); }
ifstream in;
in.open(input.c_str(), ios::binary);
- CommonHeader* header = readCommonHeader(in);
+ CommonHeader header;
+ readCommonHeader(in, header);
+
+ int count = 0;
- //cout << "magic = " << header->magicNumber << endl << "version = " << header->version << endl << "index offset = " << header->indexOffset << endl << "index length = "<< header->indexLength << endl << "numreads = " << header->numReads << endl << "header length = " << header->headerLength << endl << "key length = " << header->keyLength << endl;
-//cout << "numflowreads = "<< header->numFlowsPerRead << endl << "flow format code = "<< header->flogramFormatCode << endl << "flow chars = " << header->flowChars << endl << "key sequence = " << header->keySequence << endl << endl;
- cout << in.tellg() << endl;
+ //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()) {
-
- //read header
- Header* readheader = readHeader(in);
- //read data
- seqRead* read = readSeqData(in, header->numFlowsPerRead, readheader->numBases);
+ bool print = true;
- cout << in.tellg() << endl;
+ //read header
+ Header readheader;
+ readHeader(in, readheader);
- //print common header
- printCommonHeader(out, header, true);
+ //read data
+ seqRead read;
+ readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
+
+ //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, readheader); }
+ if (fasta) { printFastaSeqData(outFasta, read, readheader); }
+ if (qual) { printQualSeqData(outQual, read, readheader); }
+ if (flow) { printFlowSeqData(outFlow, read, readheader); }
+ }
- //print header
- printHeader(out, readheader, true);
+ count++;
+
+ //report progress
+ if((count+1) % 10000 == 0){ m->mothurOut(toString(count+1)); m->mothurOutEndLine(); }
+
+ if (m->control_pressed) { count = 0; break; }
- //print data
- printSeqData(out, read, true);
-
+ if (count >= header.numReads) { break; }
}
+ //report progress
+ if (!m->control_pressed) { if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } }
in.close();
- out.close();
- return 0;
+ if (sfftxt) { outSfftxt.close(); }
+ if (fasta) { outFasta.close(); }
+ if (qual) { outQual.close(); }
+ if (flow) { outFlow.close(); }
+
+ return count;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "extractSffInfo");
}
}
//**********************************************************************************************************************
-CommonHeader* SffInfoCommand::readCommonHeader(ifstream& in){
+int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
try {
- CommonHeader* header = new CommonHeader();
-
+
if (!in.eof()) {
- string tempBuf = "";
-
+
//read magic number
- char* buffer = new char(sizeof(header->magicNumber));
- in.read(buffer, sizeof(header->magicNumber));
- header->magicNumber = be_int4(*(uint32_t *)(buffer));
- delete[] buffer;
-
+ char buffer[4];
+ in.read(buffer, 4);
+ header.magicNumber = be_int4(*(unsigned int *)(&buffer));
+
//read version
- header->version = new char(4);
- in.read(header->version, 4);
- tempBuf = buffer;
- if (tempBuf.length() > 4) { tempBuf = tempBuf.substr(0, 4); strcpy(header->version, tempBuf.c_str()); }
-
+ char buffer9[4];
+ in.read(buffer9, 4);
+ header.version = "";
+ for (int i = 0; i < 4; i++) { header.version += toString((int)(buffer9[i])); }
+
//read offset
- buffer = new char(sizeof(header->indexOffset));
- in.read(buffer, sizeof(header->indexOffset));
- header->indexOffset = be_int8(*(uint64_t *)(buffer));
- delete[] buffer;
+ char buffer2 [8];
+ in.read(buffer2, 8);
+ header.indexOffset = be_int8(*(unsigned long int *)(&buffer2));
//read index length
- buffer = new char(sizeof(header->indexLength));
- in.read(buffer, sizeof(header->indexLength));
- header->indexLength = be_int4(*(uint32_t *)(buffer));
- delete[] buffer;
+ char buffer3 [4];
+ in.read(buffer3, 4);
+ header.indexLength = be_int4(*(unsigned int *)(&buffer3));
//read num reads
- buffer = new char(sizeof(header->numReads));
- in.read(buffer, sizeof(header->numReads));
- header->numReads = be_int4(*(uint32_t *)(buffer));
- delete[] buffer;
-
+ char buffer4 [4];
+ in.read(buffer4, 4);
+ header.numReads = be_int4(*(unsigned int *)(&buffer4));
+
//read header length
- buffer = new char(sizeof(header->headerLength));
- in.read(buffer, sizeof(header->headerLength));
- header->headerLength = be_int2(*(uint16_t *)(buffer));
- delete[] buffer;
-
+ char buffer5 [2];
+ in.read(buffer5, 2);
+ header.headerLength = be_int2(*(unsigned short *)(&buffer5));
+
//read key length
- buffer = new char(sizeof(header->keyLength));
- in.read(buffer, sizeof(header->keyLength));
- header->keyLength = be_int2(*(uint16_t *)(buffer));
- delete[] buffer;
-
- //read number of flow reads
- buffer = new char(sizeof(header->numFlowsPerRead));
- in.read(buffer, sizeof(header->numFlowsPerRead));
- header->numFlowsPerRead = be_int2(*(uint16_t *)(buffer));
- delete[] buffer;
+ char buffer6 [2];
+ in.read(buffer6, 2);
+ header.keyLength = be_int2(*(unsigned short *)(&buffer6));
+ //read number of flow reads
+ char buffer7 [2];
+ in.read(buffer7, 2);
+ header.numFlowsPerRead = be_int2(*(unsigned short *)(&buffer7));
+
//read format code
- buffer = new char(sizeof(header->flogramFormatCode));
- in.read(buffer, sizeof(header->flogramFormatCode));
- header->flogramFormatCode = be_int1(*(uint8_t *)(buffer));
- delete[] buffer;
+ char buffer8 [1];
+ in.read(buffer8, 1);
+ header.flogramFormatCode = (int)(buffer8[0]);
//read flow chars
- header->flowChars = new char(header->numFlowsPerRead);
- in.read(header->flowChars, header->numFlowsPerRead);
- tempBuf = buffer;
- if (tempBuf.length() > header->numFlowsPerRead) { tempBuf = tempBuf.substr(0, header->numFlowsPerRead); strcpy(header->flowChars, tempBuf.c_str()); }
+ 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
- header->keySequence = new char(header->keyLength);
- in.read(header->keySequence, header->keyLength);
- tempBuf = header->keySequence;
- if (tempBuf.length() > header->keyLength) { tempBuf = tempBuf.substr(0, header->keyLength); strcpy(header->keySequence, tempBuf.c_str()); }
+ 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 */
+ unsigned long int spotInFile = in.tellg();
+ unsigned long int spot = (spotInFile + 7)& ~7; // ~ inverts
+ in.seekg(spot);
}else{
m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
}
- return header;
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "readCommonHeader");
}
}
//**********************************************************************************************************************
-Header* SffInfoCommand::readHeader(ifstream& in){
+int SffInfoCommand::readHeader(ifstream& in, Header& header){
try {
- Header* header = new Header();
if (!in.eof()) {
- string tempBuf = "";
//read header length
- char* buffer = new char(sizeof(header->headerLength));
- in.read(buffer, sizeof(header->headerLength));
- header->headerLength = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
+ char buffer [2];
+ in.read(buffer, 2);
+ header.headerLength = be_int2(*(unsigned short *)(&buffer));
//read name length
- buffer = new char(sizeof(header->nameLength));
- in.read(buffer, sizeof(header->nameLength));
- header->nameLength = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
+ char buffer2 [2];
+ in.read(buffer2, 2);
+ header.nameLength = be_int2(*(unsigned short *)(&buffer2));
//read num bases
- buffer = new char(sizeof(header->numBases));
- in.read(buffer, sizeof(header->numBases));
- header->numBases = be_int4(*(unsigned int *)(buffer));
- delete[] buffer;
+ char buffer3 [4];
+ in.read(buffer3, 4);
+ header.numBases = be_int4(*(unsigned int *)(&buffer3));
//read clip qual left
- buffer = new char(sizeof(header->clipQualLeft));
- in.read(buffer, sizeof(header->clipQualLeft));
- header->clipQualLeft = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
+ char buffer4 [2];
+ in.read(buffer4, 2);
+ header.clipQualLeft = be_int2(*(unsigned short *)(&buffer4));
+ header.clipQualLeft = 5;
//read clip qual right
- buffer = new char(sizeof(header->clipQualRight));
- in.read(buffer, sizeof(header->clipQualRight));
- header->clipQualRight = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
+ char buffer5 [2];
+ in.read(buffer5, 2);
+ header.clipQualRight = be_int2(*(unsigned short *)(&buffer5));
//read clipAdapterLeft
- buffer = new char(sizeof(header->clipAdapterLeft));
- in.read(buffer, sizeof(header->clipAdapterLeft));
- header->clipAdapterLeft = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
+ char buffer6 [2];
+ in.read(buffer6, 2);
+ header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
//read clipAdapterRight
- buffer = new char(sizeof(header->clipAdapterRight));
- in.read(buffer, sizeof(header->clipAdapterRight));
- header->clipAdapterRight = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
-
+ char buffer7 [2];
+ in.read(buffer7, 2);
+ header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
+
//read name
- header->name = new char(header->nameLength);
- in.read(header->name, header->nameLength);
- tempBuf = header->name;
- if (tempBuf.length() > header->nameLength) { tempBuf = tempBuf.substr(0, header->nameLength); strcpy(header->name, tempBuf.c_str()); }
-
+ 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 */
+ unsigned long int spotInFile = in.tellg();
+ unsigned long int spot = (spotInFile + 7)& ~7;
+ in.seekg(spot);
+
}else{
m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
}
- return header;
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "readHeader");
}
}
//**********************************************************************************************************************
-seqRead* SffInfoCommand::readSeqData(ifstream& in, int numFlowReads, int numBases){
+int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, int numBases){
try {
- seqRead* read = new seqRead();
if (!in.eof()) {
-
- string tempBuf = "";
- char* buffer;
-
+
//read flowgram
- read->flowgram.resize(numFlowReads);
+ read.flowgram.resize(numFlowReads);
for (int i = 0; i < numFlowReads; i++) {
- buffer = new char((sizeof(unsigned short)));
- in.read(buffer, (sizeof(unsigned short)));
- read->flowgram[i] = be_int2(*(unsigned short *)(buffer));
- delete[] buffer;
+ char buffer [2];
+ in.read(buffer, 2);
+ read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
}
-
- //read flowgram
- read->flowIndex.resize(numBases);
+
+ //read flowIndex
+ read.flowIndex.resize(numBases);
for (int i = 0; i < numBases; i++) {
- buffer = new char(1);
- in.read(buffer, 1);
- read->flowgram[i] = be_int1(*(unsigned int *)(buffer));
- delete[] buffer;
+ char temp[1];
+ in.read(temp, 1);
+ read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
}
-
+
//read bases
- read->bases = new char(numBases);
- in.read(read->bases, numBases);
- tempBuf = buffer;
- if (tempBuf.length() > numBases) { tempBuf = tempBuf.substr(0, numBases); strcpy(read->bases, tempBuf.c_str()); }
-
+ 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->qualScores.resize(numBases);
+ //read qual scores
+ read.qualScores.resize(numBases);
for (int i = 0; i < numBases; i++) {
- buffer = new char(1);
- in.read(buffer, 1);
- read->qualScores[i] = be_int1(*(unsigned int *)(buffer));
- delete[] buffer;
+ char temp[1];
+ in.read(temp, 1);
+ read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
}
-
+
/* Pad to 8 chars */
- int spotInFile = in.tellg();
- cout << spotInFile << endl;
- int spot = floor((spotInFile + 7) /(float) 8) * 8;
- cout << spot << endl;
+ unsigned long int spotInFile = in.tellg();
+ unsigned long int spot = (spotInFile + 7)& ~7;
in.seekg(spot);
}else{
m->mothurOut("Error reading."); m->mothurOutEndLine();
}
- return read;
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "SffInfoCommand", "readSeqData");
}
}
//**********************************************************************************************************************
-int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader* header, bool debug) {
+int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
try {
- string output = "Common Header:\nMagic Number: ";
- output += toString(header->magicNumber) + '\n';
- output += "Version: " + toString(header->version) + '\n';
- output += "Index Offset: " + toString(header->indexOffset) + '\n';
- output += "Index Length: " + toString(header->indexLength) + '\n';
- output += "Number of Reads: " + toString(header->numReads) + '\n';
- output += "Header Length: " + toString(header->headerLength) + '\n';
- output += "Key Length: " + toString(header->keyLength) + '\n';
- output += "Number of Flows: " + toString(header->numFlowsPerRead) + '\n';
- output += "Format Code: " + toString(header->flogramFormatCode) + '\n';
- output += "Flow Chars: " + toString(header->flowChars) + '\n';
- output += "Key Sequence: " + toString(header->keySequence) + '\n';
-
- out << output << endl;
-
- if (debug) { cout << output << endl; }
+ out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
+ out << "Version: " << header.version << endl;
+ out << "Index Offset: " << header.indexOffset << endl;
+ out << "Index Length: " << header.indexLength << endl;
+ out << "Number of Reads: " << header.numReads << endl;
+ out << "Header Length: " << header.headerLength << endl;
+ out << "Key Length: " << header.keyLength << endl;
+ out << "Number of Flows: " << header.numFlowsPerRead << endl;
+ out << "Format Code: " << header.flogramFormatCode << endl;
+ out << "Flow Chars: " << header.flowChars << endl;
+ out << "Key Sequence: " << header.keySequence << endl << endl;
return 0;
}
}
}
//**********************************************************************************************************************
-int SffInfoCommand::printHeader(ofstream& out, Header* header, bool debug) {
+int SffInfoCommand::printHeader(ofstream& out, Header& header) {
try {
- string name = header->name;
- string output = ">" + name + "\nRead Header Length: " + toString(header->headerLength) + '\n';
- output += "Name Length: " + toString(header->nameLength) + '\n';
- output += "Number of Bases: " + toString(header->numBases) + '\n';
- output += "Clip Qual Left: " + toString(header->clipQualLeft) + '\n';
- output += "Clip Qual Right: " + toString(header->clipQualLeft) + '\n';
- output += "Clip Adap Left: " + toString(header->clipQualLeft) + '\n';
- output += "Clip Adap Right: " + toString(header->clipQualLeft) + '\n';
-
- out << output << endl;
-
- if (debug) { cout << output << endl; }
-
+
+ out << ">" << header.name << endl;
+ out << "Run Prefix: " << endl;
+ out << "Region #: " << endl;
+ out << "XY Location: " << endl << endl;
+
+ out << "Run Name: " << endl;
+ out << "Analysis Name: " << endl;
+ out << "Full Path: " << endl << endl;
+
+ out << "Read Header Len: " << header.headerLength << endl;
+ out << "Name Length: " << header.nameLength << endl;
+ out << "# of Bases: " << header.numBases << endl;
+ out << "Clip Qual Left: " << header.clipQualLeft << endl;
+ out << "Clip Qual Right: " << header.clipQualRight << endl;
+ out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
+ out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
+
return 0;
}
catch(exception& e) {
}
//**********************************************************************************************************************
-int SffInfoCommand::printSeqData(ofstream& out, seqRead* read, bool debug) {
+int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
+ try {
+
+ 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
+ if(header.clipQualRight == 0){ header.clipQualRight = read.bases.length(); }
+ 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", "printSffTxtSeqData");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
try {
+
+ string seq = read.bases;
+
+ if (trim) {
+ if(header.clipQualRight < header.clipQualLeft){
+ seq = "NNNN";
+ }
+ else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 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);
+ }
+}
- string output = "FlowGram: ";
- for (int i = 0; i < read->flowgram.size(); i++) { output += toString(read->flowgram[i]) +'\t'; }
- output += "\nFlow Indexes: ";
- for (int i = 0; i < read->flowIndex.size(); i++) { output += toString(read->flowIndex[i]) +'\t'; }
- string bases = read->bases;
- output += "\nBases: " + bases + '\n';
- for (int i = 0; i < read->qualScores.size(); i++) { output += toString(read->qualScores[i]) +'\t'; }
- output += '\n';
+//**********************************************************************************************************************
+int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
+ try {
+
+ if (trim) {
+ if(header.clipQualRight < header.clipQualLeft){
+ out << "0\t0\t0\t0";
+ }
+ else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 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 << output << endl;
+ out << endl;
- if (debug) { cout << output << 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;
+ m->openInputFile(filename, in);
+ string name;
+
+ while(!in.eof()){
+ in >> name; m->gobble(in);
+
+ seqNames.insert(name);
+
+ if (m->control_pressed) { seqNames.clear(); break; }
+ }
+ in.close();
return 0;
}
catch(exception& e) {
- m->errorOut(e, "SffInfoCommand", "printSeqData");
+ m->errorOut(e, "SffInfoCommand", "readAccnosFile");
exit(1);
}
}
projects / mothur.git / blobdiff