#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) {
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);
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]); }
string seq = read.bases;
if (trim) {
- if(header.clipQualRight != 0){
+ 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 {
try {
if (trim) {
- if(header.clipQualRight != 0){
+ 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'; }
}
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);
projects / mothur.git / blobdiff