#include "needlemanoverlap.hpp"
//**********************************************************************************************************************
+
vector<string> TrimSeqsCommand::getValidParameters(){
try {
string Array[] = {"fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile",
- "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
+ "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
+ "keepfirst", "removelast",
+ "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
return myArray;
}
exit(1);
}
}
+
//**********************************************************************************************************************
+
TrimSeqsCommand::TrimSeqsCommand(){
try {
abort = true;
exit(1);
}
}
+
//**********************************************************************************************************************
+
vector<string> TrimSeqsCommand::getRequiredParameters(){
try {
string Array[] = {"fasta"};
exit(1);
}
}
+
//**********************************************************************************************************************
+
vector<string> TrimSeqsCommand::getRequiredFiles(){
try {
vector<string> myArray;
exit(1);
}
}
+
//***************************************************************************************************************
TrimSeqsCommand::TrimSeqsCommand(string option) {
else {
//valid paramters for this command
- string AlignArray[] = {"fasta", "flip", "group","oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
- "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
+ string AlignArray[] = { "fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile",
+ "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
+ "keepfirst", "removelast",
+ "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; }
convert(temp, qWindowAverage);
- temp = validParameter.validFile(parameters, "qwindowsize", false); if (temp == "not found") { temp = "100"; }
+ temp = validParameter.validFile(parameters, "qwindowsize", false); if (temp == "not found") { temp = "50"; }
convert(temp, qWindowSize);
- temp = validParameter.validFile(parameters, "qstepsize", false); if (temp == "not found") { temp = "10"; }
+ temp = validParameter.validFile(parameters, "qstepsize", false); if (temp == "not found") { temp = "1"; }
convert(temp, qWindowStep);
temp = validParameter.validFile(parameters, "qaverage", false); if (temp == "not found") { temp = "0"; }
convert(temp, qAverage);
+
+ temp = validParameter.validFile(parameters, "keepfirst", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, keepFirst);
+
+ temp = validParameter.validFile(parameters, "removelast", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, removeLast);
temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
allFiles = m->isTrue(temp);
exit(1);
}
}
+
//**********************************************************************************************************************
void TrimSeqsCommand::help(){
outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
getOligos(fastaFileNames, qualFileNames);
}
-
+
vector<unsigned long int> fastaFilePos;
vector<unsigned long int> qFilePos;
#endif
if (m->control_pressed) { return 0; }
-
- for(int i=0;i<fastaFileNames.size();i++){
- if (m->isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str()); }
+ set<string> blanks;
+ for(int i=0;i<fastaFileNames.size();i++){
+ if (m->isBlank(fastaFileNames[i])) { blanks.insert(fastaFileNames[i]); }
else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
else {
ifstream inFASTA;
m->openInputFile(fastaFileNames[i], inFASTA);
ofstream outGroups;
string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
+
+ //if the fastafile is on the blanks list then the groups file should be as well
+ if (blanks.count(fastaFileNames[i]) != 0) { blanks.insert(outGroupFilename); }
+
m->openOutputFile(outGroupFilename, outGroups);
outputNames.push_back(outGroupFilename); outputTypes["group"].push_back(outGroupFilename);
}
}
+ for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) { remove((*(itBlanks)).c_str()); }
+
+ blanks.clear();
if(qFileName != ""){
for(int i=0;i<qualFileNames.size();i++){
- if (m->isBlank(qualFileNames[i])) { remove(qualFileNames[i].c_str()); }
+ if (m->isBlank(qualFileNames[i])) { blanks.insert(qualFileNames[i]); }
else if (filesToRemove.count(qualFileNames[i]) > 0) { remove(qualFileNames[i].c_str()); }
- else {
- ifstream inQual;
- string seqName;
- m->openInputFile(qualFileNames[i], inQual);
-// ofstream outGroups;
-//
-// string thisGroup = "";
-// if (i > comboStarts) {
-// map<string, int>::iterator itCombo;
-// for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
-// if(itCombo->second == i){ thisGroup = itCombo->first; combos.erase(itCombo); break; }
-// }
-// }
-// else{ thisGroup = groupVector[i]; }
-
- inQual.close();
- }
}
}
+ for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) { remove((*(itBlanks)).c_str()); }
if (m->control_pressed) {
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
try {
ofstream outFASTA;
- int able = m->openOutputFile(trimFile, outFASTA);
+ m->openOutputFile(trimFile, outFASTA);
ofstream scrapFASTA;
m->openOutputFile(scrapFile, scrapFASTA);
string trashCode = "";
int currentSeqsDiffs = 0;
- if(qFileName != ""){
- if(qThreshold != 0) { success = currQual.stripQualThreshold(currSeq, qThreshold); }
- else if(qAverage != 0) { success = currQual.cullQualAverage(currSeq, qAverage); }
- else if(qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, qRollAverage); }
- else if(qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage); }
-
- if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) {
- success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
- }
-
- if(!success) { trashCode += 'q'; }
- }
-
if(barcodes.size() != 0){
success = stripBarcode(currSeq, currQual, groupBar);
if(success > bdiffs) { trashCode += 'b'; }
else{ currentSeqsDiffs += success; }
}
-
+
if(numFPrimers != 0){
success = stripForward(currSeq, currQual, groupPrime);
if(success > pdiffs) { trashCode += 'f'; }
}
if (currentSeqsDiffs > tdiffs) { trashCode += 't'; }
-
+
if(numRPrimers != 0){
success = stripReverse(currSeq, currQual);
if(!success) { trashCode += 'r'; }
}
+
+ if(keepFirst != 0){
+ success = keepFirstTrim(currSeq, currQual);
+ }
+
+ if(removeLast != 0){
+ success = removeLastTrim(currSeq, currQual);
+ if(!success) { trashCode += 'l'; }
+ }
+
+
+ if(qFileName != ""){
+ int origLength = currSeq.getNumBases();
+
+ if(qThreshold != 0) { success = currQual.stripQualThreshold(currSeq, qThreshold); }
+ else if(qAverage != 0) { success = currQual.cullQualAverage(currSeq, qAverage); }
+ else if(qRollAverage != 0) { success = currQual.stripQualRollingAverage(currSeq, qRollAverage); }
+ else if(qWindowAverage != 0){ success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage); }
+ else { success = 1; }
+
+ //you don't want to trim, if it fails above then scrap it
+ if ((!qtrim) && (origLength != currSeq.getNumBases())) { success = 0; }
+
+ if(!success) { trashCode += 'q'; }
+ }
if(minLength > 0 || maxLength > 0){
success = cullLength(currSeq);
if(!success) { trashCode += 'n'; }
}
- if(flip){ currSeq.reverseComplement(); currQual.flipQScores(); } // should go last
+ if(flip){ // should go last
+ currSeq.reverseComplement();
+ currQual.flipQScores();
+ }
if(trashCode.length() == 0){
currSeq.setAligned(currSeq.getUnaligned());
//append files
for(int i=0;i<processIDS.size();i++){
- m->mothurOut("Appending files from process " + processIDS[i]); m->mothurOutEndLine();
+
+ m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
m->appendFiles((trimFile + toString(processIDS[i]) + ".temp"), trimFile);
remove((trimFile + toString(processIDS[i]) + ".temp").c_str());
exit(1);
}
}
+
//***************************************************************************************************************
void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
- int newStart=0;
int numDiff = countDiffs(oligo, temp);
// cout << oligo << '\t' << temp << '\t' << numDiff << endl;
seq.setUnaligned(rawSequence.substr(oligo.length()));
if(qual.getName() != ""){
qual.trimQScores(oligo.length(), -1);
-
}
success = 0;
break;
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
- int newStart=0;
int numDiff = countDiffs(oligo, temp);
// cout << oligo << '\t' << temp << '\t' << numDiff << endl;
//***************************************************************************************************************
+bool TrimSeqsCommand::keepFirstTrim(Sequence& sequence, QualityScores& qscores){
+ try {
+ bool success = 1;
+ if(qscores.getName() != ""){
+ qscores.trimQScores(-1, keepFirst);
+ }
+ sequence.trim(keepFirst);
+ return success;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "keepFirstTrim", "countDiffs");
+ exit(1);
+ }
+
+}
+
+//***************************************************************************************************************
+
+bool TrimSeqsCommand::removeLastTrim(Sequence& sequence, QualityScores& qscores){
+ try {
+ bool success = 0;
+
+ int length = sequence.getNumBases() - removeLast;
+
+ if(length > 0){
+ if(qscores.getName() != ""){
+ qscores.trimQScores(-1, length);
+ }
+ sequence.trim(length);
+ success = 1;
+ }
+ else{
+ success = 0;
+ }
+
+ return success;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "removeLastTrim", "countDiffs");
+ exit(1);
+ }
+
+}
+
+//***************************************************************************************************************
+
bool TrimSeqsCommand::cullLength(Sequence& seq){
try {
}
}
+
//***************************************************************************************************************
int TrimSeqsCommand::countDiffs(string oligo, string seq){
}
}
-//***************************************************************************************************************
-
-//bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
-// try {
-//
-// string rawSequence = seq.getUnaligned();
-// int seqLength = seq.getNumBases();
-// bool success = 0; //guilty until proven innocent
-// string name;
-//
-// qFile >> name;
-// if (name[0] == '>') { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } }
-//
-// while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
-//
-// int score;
-// int end = seqLength;
-//
-// for(int i=0;i<seqLength;i++){
-// qFile >> score;
-//
-// if(score < qThreshold){
-// end = i;
-// break;
-// }
-// }
-// for(int i=end+1;i<seqLength;i++){
-// qFile >> score;
-// }
-//
-// seq.setUnaligned(rawSequence.substr(0,end));
-//
-// return 1;
-// }
-// catch(exception& e) {
-// m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
-// exit(1);
-// }
-//}
-
-//***************************************************************************************************************
-
-//bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
-// try {
-// string rawSequence = seq.getUnaligned();
-// int seqLength = seq.getNumBases();
-// bool success = 0; //guilty until proven innocent
-// string name;
-//
-// qFile >> name;
-// if (name[0] == '>') { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); } }
-//
-// while (!qFile.eof()) { char c = qFile.get(); if (c == 10 || c == 13){ break; } }
-//
-// float score;
-// float average = 0;
-//
-// for(int i=0;i<seqLength;i++){
-// qFile >> score;
-// average += score;
-// }
-// average /= seqLength;
-//
-// if(average >= qAverage) { success = 1; }
-// else { success = 0; }
-//
-// return success;
-// }
-// catch(exception& e) {
-// m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
-// exit(1);
-// }
-//}
//***************************************************************************************************************
projects / mothur.git / blobdiff