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) {
//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 */
- 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::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 != 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 != 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'; }
projects / mothur.git / blobdiff