CommandParameter pfile("file", "InputTypes", "", "", "sffFastQFile-oligos", "sffFastQFile", "none","xml",false,false); parameters.push_back(pfile);
CommandParameter pfastq("fastq", "InputTypes", "", "", "sffFastQFile", "sffFastQFile", "none","xml",false,false); parameters.push_back(pfastq);
CommandParameter pcontact("project", "InputTypes", "", "", "none", "none", "none","xml",false,true,true); parameters.push_back(pcontact);
+ CommandParameter preorient("checkorient", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(preorient);
CommandParameter pmimark("mimark", "InputTypes", "", "", "none", "none", "none","xml",false,true,true); parameters.push_back(pmimark);
//choose only one multiple options
CommandParameter pplatform("platform", "Multiple", "_LS454-ILLUMINA-ION_TORRENT-PACBIO_SMRT", "_LS454", "", "", "","",false,false); parameters.push_back(pplatform);
try {
string helpString = "";
helpString += "The sra command creates the necessary files for a NCBI submission. The xml file and individual sff or fastq files parsed from the original sff or fastq file.\n";
- helpString += "The sra command parameters are: sff, fastq, file, oligos, project, mimarksfile, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, platform, orientation, libstrategy, datatype, libsource, libselection and instrument.\n";
+ helpString += "The sra command parameters are: sff, fastq, file, oligos, project, mimarksfile, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, checkorient, platform, orientation, libstrategy, datatype, libsource, libselection and instrument.\n";
helpString += "The sff parameter is used to provide the original sff file.\n";
helpString += "The fastq parameter is used to provide the original fastq file.\n";
helpString += "The project parameter is used to provide your project file.\n";
helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
+ helpString += "The checkorient parameter will check look for the reverse compliment of the barcode or primer in the sequence. The default is false.\n";
helpString += "The platform parameter is used to specify platform you are using choices are: _LS454,ILLUMINA,ION_TORRENT,PACBIO_SMRT. Default=_LS454. This is a controlled vocabulary section in the XML file that will be generated.\n";
helpString += "The orientation parameter is used to specify sequence orientation. Choices are: forward and reverse. Default=forward. This is a controlled vocabulary section in the XML file that will be generated.\n";
helpString += "The instrument parameter is used to specify instrument. Choices are 454_GS-454_GS_20-454_GS_FLX-454_GS_FLX_Titanium-454_GS_Junior-Illumina_Genome_Analyzer-Illumina_Genome_Analyzer_II-Illumina_Genome_Analyzer_IIx-Illumina_HiSeq_2000-Illumina_HiSeq_1000-Illumina_MiSeq-PacBio_RS-Ion_Torrent_PGM-unspecified. Default=454_GS. This is a controlled vocabulary section in the XML file that will be generated. \n";
outputTypes["xml"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
- string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
else {
m->mothurConvert(temp, tdiffs);
if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
+
+ checkorient = validParameter.validFile(parameters, "checkorient", false); if (temp == "not found") { temp = "F"; }
}
if (m->debug) { m->mothurOut("[DEBUG]: group = " + group + ", thisFileName1 = " + thisFileName1 + ", thisFileName2 = " + thisFileName2 + ".\n"); }
+ if (inputDir != "") {
+ string path = m->hasPath(thisFileName1);
+ if (path == "") { thisFileName1 = inputDir + thisFileName1; }
+
+ path = m->hasPath(thisFileName2);
+ if (path == "") { thisFileName2 = inputDir + thisFileName2; }
+ }
+
//check to make sure both are able to be opened
ifstream in2;
int openForward = m->openInputFile(thisFileName1, in2, "noerror");
//if you can't open it, try default location
if (openForward == 1) {
+
if (m->getDefaultPath() != "") { //default path is set
string tryPath = m->getDefaultPath() + m->getSimpleName(thisFileName1);
m->mothurOut("Unable to open " + thisFileName1 + ". Trying default " + tryPath); m->mothurOutEndLine();
if (ldiffs != 0) { commandString += ", ldiffs=" + toString(ldiffs); }
if (sdiffs != 0) { commandString += ", sdiffs=" + toString(sdiffs); }
if (tdiffs != 0) { commandString += ", tdiffs=" + toString(tdiffs); }
+ if (m->isTrue(checkorient)) { commandString += ", checkorient=" + checkorient; }
m->mothurOutEndLine();
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
if (ldiffs != 0) { commandString += ", ldiffs=" + toString(ldiffs); }
if (sdiffs != 0) { commandString += ", sdiffs=" + toString(sdiffs); }
if (tdiffs != 0) { commandString += ", tdiffs=" + toString(tdiffs); }
+ if (m->isTrue(checkorient)) { commandString += ", checkorient=" + checkorient; }
m->mothurOutEndLine();
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
//***************************************************************************************************************
int SRACommand::readOligos(){
try {
- ifstream inOligos;
- m->openInputFile(oligosfile, inOligos);
-
- string type, oligo, roligo, group;
- bool hasPrimer = false; bool hasPairedBarcodes = false; pairedOligos = false;
- map<int, oligosPair> pairedBarcodes;
- map<int, oligosPair> pairedPrimers;
- map<string, int> barcodes;
- map<string, int> primers;
- vector<string> linker;
- vector<string> spacer, revPrimer;
- int indexPrimer = 0;
- int indexBarcode = 0;
- int indexPairedPrimer = 0;
- int indexPairedBarcode = 0;
- set<string> uniquePrimers;
- set<string> uniqueBarcodes;
-
- while(!inOligos.eof()){
-
- inOligos >> type;
-
- if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
-
- if(type[0] == '#'){
- while (!inOligos.eof()) { char c = inOligos.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
- m->gobble(inOligos);
- }
- else{
- m->gobble(inOligos);
- //make type case insensitive
- for(int i=0;i<type.length();i++){ type[i] = toupper(type[i]); }
-
- inOligos >> oligo;
-
- if (m->debug) { m->mothurOut("[DEBUG]: reading - " + oligo + ".\n"); }
-
- for(int i=0;i<oligo.length();i++){
- oligo[i] = toupper(oligo[i]);
- if(oligo[i] == 'U') { oligo[i] = 'T'; }
- }
-
- if(type == "FORWARD"){
- group = "";
-
- // get rest of line in case there is a primer name
- while (!inOligos.eof()) {
- char c = inOligos.get();
- if (c == 10 || c == 13 || c == -1){ break; }
- else if (c == 32 || c == 9){;} //space or tab
- else { group += c; }
- }
-
- //check for repeat barcodes
- map<string, int>::iterator itPrime = primers.find(oligo);
- if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
-
- if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer " + oligo + ".\n"); } }
-
- primers[oligo] = indexPrimer; indexPrimer++;
- primerNameVector.push_back(group);
- }
- else if (type == "PRIMER"){
- m->gobble(inOligos);
-
- inOligos >> roligo;
-
- for(int i=0;i<roligo.length();i++){
- roligo[i] = toupper(roligo[i]);
- if(roligo[i] == 'U') { roligo[i] = 'T'; }
- }
- roligo = reverseOligo(roligo);
-
- group = "";
-
- // get rest of line in case there is a primer name
- while (!inOligos.eof()) {
- char c = inOligos.get();
- if (c == 10 || c == 13 || c == -1){ break; }
- else if (c == 32 || c == 9){;} //space or tab
- else { group += c; }
- }
-
- oligosPair newPrimer(oligo, roligo);
-
- if (m->debug) { m->mothurOut("[DEBUG]: primer pair " + newPrimer.forward + " " + newPrimer.reverse + ", and group = " + group + ".\n"); }
-
- //check for repeat barcodes
- string tempPair = oligo+roligo;
- if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine(); }
- else { uniquePrimers.insert(tempPair); }
-
- if (m->debug) { if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); } }
-
- pairedPrimers[indexPairedPrimer]=newPrimer; indexPairedPrimer++;
- primerNameVector.push_back(group);
- hasPrimer = true;
- }
- else if(type == "REVERSE"){
- //Sequence oligoRC("reverse", oligo);
- //oligoRC.reverseComplement();
- string oligoRC = reverseOligo(oligo);
- revPrimer.push_back(oligoRC);
- }
- else if(type == "BARCODE"){
- inOligos >> group;
-
- //barcode lines can look like BARCODE atgcatgc groupName - for 454 seqs
- //or BARCODE atgcatgc atgcatgc groupName - for illumina data that has forward and reverse info
-
- string temp = "";
- while (!inOligos.eof()) {
- char c = inOligos.get();
- if (c == 10 || c == 13 || c == -1){ break; }
- else if (c == 32 || c == 9){;} //space or tab
- else { temp += c; }
- }
-
- //then this is illumina data with 4 columns
- if (temp != "") {
- hasPairedBarcodes = true;
- string reverseBarcode = group; //reverseOligo(group); //reverse barcode
- group = temp;
-
- for(int i=0;i<reverseBarcode.length();i++){
- reverseBarcode[i] = toupper(reverseBarcode[i]);
- if(reverseBarcode[i] == 'U') { reverseBarcode[i] = 'T'; }
- }
-
- reverseBarcode = reverseOligo(reverseBarcode);
- oligosPair newPair(oligo, reverseBarcode);
-
- if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
- //check for repeat barcodes
- string tempPair = oligo+reverseBarcode;
- if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse + " is in your oligos file already, disregarding."); m->mothurOutEndLine(); }
- else { uniqueBarcodes.insert(tempPair); }
-
- pairedBarcodes[indexPairedBarcode]=newPair; indexPairedBarcode++;
- barcodeNameVector.push_back(group);
- }else {
- //check for repeat barcodes
- map<string, int>::iterator itBar = barcodes.find(oligo);
- if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine(); }
-
- barcodes[oligo]=indexBarcode; indexBarcode++;
- barcodeNameVector.push_back(group);
- }
- }else if(type == "LINKER"){
- linker.push_back(oligo);
- }else if(type == "SPACER"){
- spacer.push_back(oligo);
- }
- else{ m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
- }
- m->gobble(inOligos);
- }
- inOligos.close();
-
- if (hasPairedBarcodes || hasPrimer) {
- pairedOligos = true;
- if ((primers.size() != 0) || (barcodes.size() != 0) || (linker.size() != 0) || (spacer.size() != 0) || (revPrimer.size() != 0)) { m->control_pressed = true; m->mothurOut("[ERROR]: cannot mix paired primers and barcodes with non paired or linkers and spacers, quitting."); m->mothurOutEndLine(); return 0; }
- }
-
+ Oligos oligos(oligosfile);
- //add in potential combos
- if(barcodeNameVector.size() == 0){
- barcodeNameVector.push_back("");
- }
-
- if(primerNameVector.size() == 0){
- primerNameVector.push_back("");
- }
+ if (m->control_pressed) { return false; } //error in reading oligos
+
+ if (oligos.hasPairedBarcodes()) { pairedOligos = true; }
+ else { pairedOligos = false; }
+ set<string> uniqueNames; //used to cleanup outputFileNames
if (pairedOligos) {
- for(map<int, oligosPair>::iterator itBar = pairedBarcodes.begin();itBar != pairedBarcodes.end();itBar++){
- for(map<int, oligosPair>::iterator itPrimer = pairedPrimers.begin();itPrimer != pairedPrimers.end(); itPrimer++){
+ map<int, oligosPair> barcodes = oligos.getPairedBarcodes();
+ map<int, oligosPair> primers = oligos.getPairedPrimers();
+ for(map<int, oligosPair>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
+ for(map<int, oligosPair>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
- string primerName = primerNameVector[itPrimer->first];
- string barcodeName = barcodeNameVector[itBar->first];
+ string primerName = oligos.getPrimerName(itPrimer->first);
+ string barcodeName = oligos.getBarcodeName(itBar->first);
if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else if ((primerName == "") && (barcodeName == "")) { } //do nothing
else {
string comboGroupName = "";
- string fastqFileName = "";
+ string fastaFileName = "";
+ string qualFileName = "";
+ string nameFileName = "";
+ string countFileName = "";
if(primerName == ""){
- comboGroupName = barcodeNameVector[itBar->first];
- }
- else{
+ comboGroupName = barcodeName;
+ }else{
if(barcodeName == ""){
- comboGroupName = primerNameVector[itPrimer->first];
+ comboGroupName = primerName;
}
else{
- comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
+ comboGroupName = barcodeName + "." + primerName;
}
}
uniqueNames.insert(comboGroupName);
}
}
}else {
+ map<string, int> barcodes = oligos.getBarcodes() ;
+ map<string, int> primers = oligos.getPrimers();
for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
- string primerName = primerNameVector[itPrimer->second];
- string barcodeName = barcodeNameVector[itBar->second];
+ string primerName = oligos.getPrimerName(itPrimer->second);
+ string barcodeName = oligos.getBarcodeName(itBar->second);
if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else if ((primerName == "") && (barcodeName == "")) { } //do nothing
else {
string comboGroupName = "";
- string fastqFileName = "";
+ string fastaFileName = "";
+ string qualFileName = "";
+ string nameFileName = "";
+ string countFileName = "";
if(primerName == ""){
- comboGroupName = barcodeNameVector[itBar->second];
- }
- else{
+ comboGroupName = barcodeName;
+ }else{
if(barcodeName == ""){
- comboGroupName = primerNameVector[itPrimer->second];
+ comboGroupName = primerName;
}
else{
- comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
+ comboGroupName = barcodeName + "." + primerName;
}
}
uniqueNames.insert(comboGroupName);
}
}
}
-
-
- if (m->debug) { int count = 0; for (set<string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) { m->mothurOut("[DEBUG]: " + toString(count) + " groupName = " + *it + "\n"); count++; } }
+ if (m->debug) { int count = 0; for (set<string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) { m->mothurOut("[DEBUG]: " + toString(count) + " groupName = " + *it + "\n"); count++; } }
return true;
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