#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 {
+ abort = true;
+ //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) {
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, "noerror");
+ 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() + getSimpleName(filenames[i]);
+ string tryPath = m->getDefaultPath() + m->getSimpleName(filenames[i]);
m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ableToOpen = openInputFile(tryPath, in, "noerror");
+ 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) {
if (accnosName == "not found") { accnosName = ""; }
else {
hasAccnos = true;
- splitAtDash(accnosName, accnosFileNames);
+ 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 = hasPath(accnosFileNames[i]);
+ 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 = openInputFile(accnosFileNames[i], in, "noerror");
+ 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() + getSimpleName(accnosFileNames[i]);
+ string tryPath = m->getDefaultPath() + m->getSimpleName(accnosFileNames[i]);
m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ableToOpen = openInputFile(tryPath, in, "noerror");
+ 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;
}
}
}
string temp = validParameter.validFile(parameters, "qfile", false); if (temp == "not found"){ temp = "T"; }
- qual = isTrue(temp);
+ qual = m->isTrue(temp);
temp = validParameter.validFile(parameters, "fasta", false); if (temp == "not found"){ temp = "T"; }
- fasta = isTrue(temp);
+ fasta = m->isTrue(temp);
temp = validParameter.validFile(parameters, "flow", false); if (temp == "not found"){ temp = "F"; }
- flow = isTrue(temp);
+ flow = m->isTrue(temp);
temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found"){ temp = "T"; }
- trim = isTrue(temp);
+ trim = m->isTrue(temp);
temp = validParameter.validFile(parameters, "sfftxt", false); if (temp == "not found"){ temp = "F"; }
- sfftxt = isTrue(temp);
+ sfftxt = m->isTrue(temp);
}
}
catch(exception& e) {
int SffInfoCommand::extractSffInfo(string input, string accnos){
try {
- if (outputDir == "") { outputDir += hasPath(input); }
+ if (outputDir == "") { outputDir += m->hasPath(input); }
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";
+ string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
+ string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
if (trim) {
- outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "fasta";
- outQualFileName = outputDir + getRootName(getSimpleName(input)) + "qual";
+ outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "fasta";
+ outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "qual";
}else{
- outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "raw.fasta";
- outQualFileName = outputDir + getRootName(getSimpleName(input)) + "raw.qual";
+ outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.fasta";
+ outQualFileName = outputDir + m->getRootName(m->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); }
+ 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);
//print common header
if (sfftxt) { printCommonHeader(outSfftxt, header); }
-
+
//read through the sff file
while (!in.eof()) {
//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); }
+ 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();
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 */
unsigned long int spotInFile = in.tellg();
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 */
unsigned long int spotInFile = in.tellg();
//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 */
unsigned long int spotInFile = in.tellg();
unsigned long int spot = (spotInFile + 7)& ~7;
}
//**********************************************************************************************************************
-int SffInfoCommand::printSffTxtSeqData(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
+ 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;
string seq = read.bases;
-
if (trim) {
- seq = seq.substr(header.clipQualLeft, (header.clipQualRight-header.clipQualLeft));
+ 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;
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'; }
+ 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'; }
seqNames.clear();
ifstream in;
- openInputFile(filename, in);
+ m->openInputFile(filename, in);
string name;
while(!in.eof()){
- in >> name; gobble(in);
+ in >> name; m->gobble(in);
seqNames.insert(name);
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