--- /dev/null
+//
+// oligos.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 4/4/14.
+// Copyright (c) 2014 Schloss Lab. All rights reserved.
+//
+
+#include "oligos.h"
+
+/**************************************************************************************************/
+
+Oligos::Oligos(string o){
+ try {
+ m = MothurOut::getInstance();
+ hasPPrimers = false; hasPBarcodes = false; pairedOligos = false; reversePairs = true;
+ indexBarcode = 0; indexPairedBarcode = 0; indexPrimer = 0; indexPairedPrimer = 0;
+ oligosfile = o;
+ readOligos();
+ if (pairedOligos) {
+ numBarcodes = pairedBarcodes.size();
+ numFPrimers = pairedPrimers.size();
+ }else {
+ numBarcodes = barcodes.size();
+ numFPrimers = primers.size();
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Oligos", "Oligos");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+Oligos::Oligos(){
+ try {
+ m = MothurOut::getInstance();
+ hasPPrimers = false; hasPBarcodes = false; pairedOligos = false; reversePairs = true;
+ indexBarcode = 0; indexPairedBarcode = 0; indexPrimer = 0; indexPairedPrimer = 0;
+ numFPrimers = 0; numBarcodes = 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Oligos", "Oligos");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int Oligos::read(string o){
+ try {
+ oligosfile = o;
+ readOligos();
+ if (pairedOligos) {
+ numBarcodes = pairedBarcodes.size();
+ numFPrimers = pairedPrimers.size();
+ }else {
+ numBarcodes = barcodes.size();
+ numFPrimers = primers.size();
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Oligos", "read");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int Oligos::read(string o, bool reverse){
+ try {
+ oligosfile = o;
+ reversePairs = reverse;
+ readOligos();
+ if (pairedOligos) {
+ numBarcodes = pairedBarcodes.size();
+ numFPrimers = pairedPrimers.size();
+ }else {
+ numBarcodes = barcodes.size();
+ numFPrimers = primers.size();
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Oligos", "read");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+int Oligos::readOligos(){
+ try {
+ ifstream inOligos;
+ m->openInputFile(oligosfile, inOligos);
+
+ string type, oligo, roligo, group;
+
+ 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("[WARNING]: 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'; }
+ }
+ if (reversePairs) { 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);
+ hasPPrimers = true;
+ }
+ else if(type == "REVERSE"){
+ 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 != "") {
+ hasPBarcodes = 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'; }
+ }
+
+ if (reversePairs) { 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("[WARNING]: 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 (hasPBarcodes || hasPPrimers) {
+ 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; }
+ }
+
+
+ //add in potential combos
+ if(barcodeNameVector.size() == 0){
+ if (pairedOligos) {
+ oligosPair newPair("", "");
+ pairedBarcodes[0] = newPair;
+ }else {
+ barcodes[""] = 0;
+ }
+ barcodeNameVector.push_back("");
+ }
+
+ if(primerNameVector.size() == 0){
+ if (pairedOligos) {
+ oligosPair newPair("", "");
+ pairedPrimers[0] = newPair;
+ }else {
+ primers[""] = 0;
+ }
+ primerNameVector.push_back("");
+ }
+
+
+ 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++){
+
+ string primerName = primerNameVector[itPrimer->first];
+ string barcodeName = barcodeNameVector[itBar->first];
+
+ if (m->debug) { m->mothurOut("[DEBUG]: primerName = " + primerName + " barcodeName = " + barcodeName + "\n"); }
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { if (m->debug) { m->mothurOut("[DEBUG]: in ignore. \n"); } } //do nothing
+ else if ((primerName == "") && (barcodeName == "")) { if (m->debug) { m->mothurOut("[DEBUG]: in blank. \n"); } } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastqFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->first];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->first];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
+ }
+ }
+
+ if (m->debug) { m->mothurOut("[DEBUG]: comboGroupName = " + comboGroupName + "\n"); }
+
+ uniqueNames.insert(comboGroupName);
+
+ map<string, vector<string> >::iterator itGroup2Barcode = Group2Barcode.find(comboGroupName);
+ if (itGroup2Barcode == Group2Barcode.end()) {
+ vector<string> tempBarcodes; tempBarcodes.push_back((itBar->second).forward+"."+(itBar->second).reverse);
+ Group2Barcode[comboGroupName] = tempBarcodes;
+ }else {
+ Group2Barcode[comboGroupName].push_back((itBar->second).forward+"."+(itBar->second).reverse);
+ }
+
+ itGroup2Barcode = Group2Primer.find(comboGroupName);
+ if (itGroup2Barcode == Group2Primer.end()) {
+ vector<string> tempPrimers; tempPrimers.push_back((itPrimer->second).forward+"."+(itPrimer->second).reverse);
+ Group2Primer[comboGroupName] = tempPrimers;
+ }else {
+ Group2Primer[comboGroupName].push_back((itPrimer->second).forward+"."+(itPrimer->second).reverse);
+ }
+ }
+ }
+ }
+ }else {
+ 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];
+
+ if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
+ else if ((primerName == "") && (barcodeName == "")) { } //do nothing
+ else {
+ string comboGroupName = "";
+ string fastqFileName = "";
+
+ if(primerName == ""){
+ comboGroupName = barcodeNameVector[itBar->second];
+ }
+ else{
+ if(barcodeName == ""){
+ comboGroupName = primerNameVector[itPrimer->second];
+ }
+ else{
+ comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
+ }
+ }
+ uniqueNames.insert(comboGroupName);
+
+ map<string, vector<string> >::iterator itGroup2Barcode = Group2Barcode.find(comboGroupName);
+ if (itGroup2Barcode == Group2Barcode.end()) {
+ vector<string> tempBarcodes; tempBarcodes.push_back(itBar->first);
+ Group2Barcode[comboGroupName] = tempBarcodes;
+ }else {
+ Group2Barcode[comboGroupName].push_back(itBar->first);
+ }
+
+ itGroup2Barcode = Group2Primer.find(comboGroupName);
+ if (itGroup2Barcode == Group2Primer.end()) {
+ vector<string> tempPrimers; tempPrimers.push_back(itPrimer->first);
+ Group2Primer[comboGroupName] = tempPrimers;
+ }else {
+ Group2Primer[comboGroupName].push_back(itPrimer->first);
+ }
+ }
+ }
+ }
+ }
+
+
+ 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++; } }
+
+
+ Groups.clear();
+ for (set<string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) { Groups.push_back(*it); }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Oligos", "readOligos");
+ exit(1);
+ }
+}
+//********************************************************************/
+vector<string> Oligos::getBarcodes(string groupName){
+ try {
+ vector<string> thisGroupsBarcodes;
+
+ map<string, vector<string> >::iterator it = Group2Barcode.find(groupName);
+
+ if (it == Group2Barcode.end()) { m->mothurOut("[ERROR]: no barcodes found for group " + groupName + ".\n"); m->control_pressed=true;
+ }else { thisGroupsBarcodes = it->second; }
+
+ return thisGroupsBarcodes;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Oligos", "getBarcodes");
+ exit(1);
+ }
+}
+//********************************************************************/
+vector<string> Oligos::getPrimers(string groupName){
+ try {
+ vector<string> thisGroupsPrimers;
+
+ map<string, vector<string> >::iterator it = Group2Primer.find(groupName);
+
+ if (it == Group2Primer.end()) { m->mothurOut("[ERROR]: no primers found for group " + groupName + ".\n"); m->control_pressed=true;
+ }else { thisGroupsPrimers = it->second; }
+
+ return thisGroupsPrimers;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Oligos", "getPrimers");
+ exit(1);
+ }
+}
+//********************************************************************/
+//can't have paired and unpaired so this function will either run the paired map or the unpaired
+map<int, oligosPair> Oligos::getReorientedPairedPrimers(){
+ try {
+ map<int, oligosPair> rpairedPrimers;
+
+ for (map<int, oligosPair>::iterator it = pairedPrimers.begin(); it != pairedPrimers.end(); it++) {
+ string forward = (it->second).reverse;
+ if (reversePairs) { forward = reverseOligo(forward); }
+ string reverse = (it->second).forward;
+ if (reversePairs) { reverse = reverseOligo(reverse); }
+ oligosPair tempPair(forward, reverse); //reversePrimer, rc ForwardPrimer
+ rpairedPrimers[it->first] = tempPair;
+ }
+
+
+ for (map<string, int>::iterator it = primers.begin(); it != primers.end(); it++) {
+ oligosPair tempPair("", reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode
+ rpairedPrimers[it->second] = tempPair;
+ }
+
+ return rpairedPrimers;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Oligos", "getReorientedPairedPrimers");
+ exit(1);
+ }
+}
+//********************************************************************/
+//can't have paired and unpaired so this function will either run the paired map or the unpaired
+map<int, oligosPair> Oligos::getReorientedPairedBarcodes(){
+ try {
+ map<int, oligosPair> rpairedBarcodes;
+
+ for (map<int, oligosPair>::iterator it = pairedBarcodes.begin(); it != pairedBarcodes.end(); it++) {
+ string forward = (it->second).reverse;
+ if (reversePairs) { forward = reverseOligo(forward); }
+ string reverse = (it->second).forward;
+ if (reversePairs) { reverse = reverseOligo(reverse); }
+ oligosPair tempPair(forward, reverse); //reversePrimer, rc ForwardPrimer
+ rpairedBarcodes[it->first] = tempPair;
+ }
+
+ for (map<string, int>::iterator it = barcodes.begin(); it != barcodes.end(); it++) {
+ oligosPair tempPair("", reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode
+ rpairedBarcodes[it->second] = tempPair;
+ }
+
+ return rpairedBarcodes;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Oligos", "getReorientedPairedBarcodes");
+ exit(1);
+ }
+}
+
+//********************************************************************/
+string Oligos::reverseOligo(string oligo){
+ try {
+ string reverse = "";
+
+ for(int i=oligo.length()-1;i>=0;i--){
+
+ if(oligo[i] == 'A') { reverse += 'T'; }
+ else if(oligo[i] == 'T'){ reverse += 'A'; }
+ else if(oligo[i] == 'U'){ reverse += 'A'; }
+
+ else if(oligo[i] == 'G'){ reverse += 'C'; }
+ else if(oligo[i] == 'C'){ reverse += 'G'; }
+
+ else if(oligo[i] == 'R'){ reverse += 'Y'; }
+ else if(oligo[i] == 'Y'){ reverse += 'R'; }
+
+ else if(oligo[i] == 'M'){ reverse += 'K'; }
+ else if(oligo[i] == 'K'){ reverse += 'M'; }
+
+ else if(oligo[i] == 'W'){ reverse += 'W'; }
+ else if(oligo[i] == 'S'){ reverse += 'S'; }
+
+ else if(oligo[i] == 'B'){ reverse += 'V'; }
+ else if(oligo[i] == 'V'){ reverse += 'B'; }
+
+ else if(oligo[i] == 'D'){ reverse += 'H'; }
+ else if(oligo[i] == 'H'){ reverse += 'D'; }
+
+ else { reverse += 'N'; }
+ }
+
+
+ return reverse;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Oligos", "reverseOligo");
+ exit(1);
+ }
+}
+//********************************************************************/
+string Oligos::getBarcodeName(int index){
+ try {
+ string name = "";
+
+ if ((index >= 0) && (index < barcodeNameVector.size())) { name = barcodeNameVector[index]; }
+
+ return name;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Oligos", "getBarcodeName");
+ exit(1);
+ }
+}
+//********************************************************************/
+string Oligos::getPrimerName(int index){
+ try {
+ string name = "";
+
+ if ((index >= 0) && (index < primerNameVector.size())) { name = primerNameVector[index]; }
+
+ return name;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Oligos", "getPrimerName");
+ exit(1);
+ }
+}
+//********************************************************************/
+string Oligos::getGroupName(int barcodeIndex, int primerIndex){
+ try {
+
+ string thisGroup = "";
+ if(numBarcodes != 0){
+ thisGroup = getBarcodeName(barcodeIndex);
+ if (numFPrimers != 0) {
+ if (getPrimerName(primerIndex) != "") {
+ if(thisGroup != "") {
+ thisGroup += "." + getPrimerName(primerIndex);
+ }else {
+ thisGroup = getPrimerName(primerIndex);
+ }
+ }
+ }
+ }
+
+ return thisGroup;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Oligos", "getGroupName");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
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