else {
//valid paramters for this command
- string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors"};
+ string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
convert(temp, processors);
+ temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; }
+ flip = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "0.80"; }
+ convert(temp, threshold);
+
search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -1.0.\n");
mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -2.0.\n");
+ mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse compement if a sequence falls below the threshold. The default is false.\n");
+ mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. \n");
+ mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
+ mothurOut("The default for the threshold parameter is 0.80, meaning at least 80% of the bases must remain or the sequence is reported as potentially reversed.\n");
mothurOut("The align.seqs command should be in the following format: \n");
mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n");
string alignFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align";
string reportFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align.report";
+ string accnosFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "flip.accnos";
int numFastaSeqs = 0;
int start = time(NULL);
lines.push_back(new linePair(0, numFastaSeqs));
- driver(lines[0], alignFileName, reportFileName);
+ driver(lines[0], alignFileName, reportFileName, accnosFileName);
+ //delete accnos file if its blank else report to user
+ if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); }
+ else {
+ mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
+ if (!flip) {
+ mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
+ }else{ mothurOut(" If the reverse compliment proved to be better it was reported."); }
+ mothurOutEndLine();
+ }
}
else{
vector<int> positions;
}
lines.push_back(new linePair(startPos, numSeqsPerProcessor));
}
- createProcesses(alignFileName, reportFileName);
+ createProcesses(alignFileName, reportFileName, accnosFileName);
rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
+ vector<string> nonBlankAccnosFiles;
+ //delete blank accnos files generated with multiple processes
+ for(int i=0;i<processors;i++){
+ if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
+ nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
+ }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str()); }
+ }
+
+ //append accnos files
+ if (nonBlankAccnosFiles.size() != 0) {
+ rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
+
+ for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
+ appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
+ remove(nonBlankAccnosFiles[h].c_str());
+ }
+ mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
+ if (!flip) {
+ mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
+ }else{ mothurOut(" If the reverse compliment proved to be better it was reported."); }
+ mothurOutEndLine();
+ }
+
+ //append other files
for(int i=1;i<processors;i++){
appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
lines.push_back(new linePair(0, numFastaSeqs));
- driver(lines[0], alignFileName, reportFileName);
+ driver(lines[0], alignFileName, reportFileName, accnosFileName);
+
+ //delete accnos file if its blank else report to user
+ if (isBlank(accnosFileName)) { remove(accnosFileName.c_str()); }
+ else {
+ mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
+ if (!flip) {
+ mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
+ }else{ mothurOut(" If the reverse compliment proved to be better it was reported."); }
+ mothurOutEndLine();
+ }
+
#endif
+
+
mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
mothurOutEndLine();
mothurOutEndLine();
//**********************************************************************************************************************
-int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
+int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName){
try {
ofstream alignmentFile;
openOutputFile(alignFName, alignmentFile);
+
+ ofstream accnosFile;
+ openOutputFile(accnosFName, accnosFile);
+
NastReport report(reportFName);
ifstream inFASTA;
for(int i=0;i<line->numSeqs;i++){
Sequence* candidateSeq = new Sequence(inFASTA);
-
- if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
- alignment->resize(candidateSeq->getUnaligned().length()+1);
- }
-
- report.setCandidate(candidateSeq);
-
- Sequence temp = templateDB->findClosestSequence(candidateSeq);
-
- Sequence* templateSeq = &temp;
-
- report.setTemplate(templateSeq);
- report.setSearchParameters(search, templateDB->getSearchScore());
+ int origNumBases = candidateSeq->getNumBases();
+ string originalUnaligned = candidateSeq->getUnaligned();
+ int numBasesNeeded = origNumBases * threshold;
+
+ if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
+ if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
+ alignment->resize(candidateSeq->getUnaligned().length()+1);
+ }
+
+ Sequence temp = templateDB->findClosestSequence(candidateSeq);
+ Sequence* templateSeq = &temp;
- Nast nast(alignment, candidateSeq, templateSeq);
-
- report.setAlignmentParameters(align, alignment);
-
- report.setNastParameters(nast);
-
- alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
+ float searchScore = templateDB->getSearchScore();
+
+ Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
+ Sequence* copy;
- report.print();
+ Nast* nast2;
+ bool needToDeleteCopy = false; //this is needed in case you have you enter the ifs below
+ //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
+ //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
+ //so this bool tells you if you need to delete it
+
+ //if there is a possibility that this sequence should be reversed
+ if (candidateSeq->getNumBases() < numBasesNeeded) {
+
+ string wasBetter = "";
+ //if the user wants you to try the reverse
+ if (flip) {
+ //get reverse compliment
+ copy = new Sequence(candidateSeq->getName(), originalUnaligned);
+ copy->reverseComplement();
+
+ //rerun alignment
+ Sequence temp2 = templateDB->findClosestSequence(copy);
+ Sequence* templateSeq2 = &temp2;
+
+ searchScore = templateDB->getSearchScore();
+
+ nast2 = new Nast(alignment, copy, templateSeq2);
+ //check if any better
+ if (copy->getNumBases() > candidateSeq->getNumBases()) {
+ candidateSeq->setAligned(copy->getAligned()); //use reverse compliments alignment since its better
+ templateSeq = templateSeq2;
+ delete nast;
+ nast = nast2;
+ needToDeleteCopy = true;
+ }else{
+ wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
+ delete nast2;
+ delete copy;
+ }
+ }
+
+ //create accnos file with names
+ accnosFile << candidateSeq->getName() << wasBetter << endl;
+ }
+
+ report.setCandidate(candidateSeq);
+ report.setTemplate(templateSeq);
+ report.setSearchParameters(search, searchScore);
+ report.setAlignmentParameters(align, alignment);
+ report.setNastParameters(*nast);
+
+ alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
+
+ report.print();
+ delete nast;
+ if (needToDeleteCopy) { delete copy; }
+ }
delete candidateSeq;
-
}
alignmentFile.close();
inFASTA.close();
+ accnosFile.close();
return 1;
}
/**************************************************************************************************/
-void AlignCommand::createProcesses(string alignFileName, string reportFileName) {
+void AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 0;
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp");
+ driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp");
exit(0);
}else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
}
exit(1);
}
}
-
-/**************************************************************************************************/
+//**********************************************************************************************************************
void AlignCommand::appendReportFiles(string temp, string filename) {
try{
projects / mothur.git / blobdiff