#include "blastalign.hpp"
#include "noalign.hpp"
-#include "kmerdb.hpp"
-#include "suffixdb.hpp"
-#include "blastdb.hpp"
-
#include "nast.hpp"
#include "nastreport.hpp"
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","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string, string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //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 = ""; }
+
+ //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);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("template");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["template"] = inputDir + it->second; }
+ }
+ }
+
//check for required parameters
templateFileName = validParameter.validFile(parameters, "template", true);
if (templateFileName == "not found") {
mothurOut("template is a required parameter for the align.seqs command.");
mothurOutEndLine();
abort = true;
- }
- else if (templateFileName == "not open") { abort = true; }
+ }else if (templateFileName == "not open") { abort = true; }
- candidateFileName = validParameter.validFile(parameters, "candidate", true);
- if (candidateFileName == "not found") {
- mothurOut("candidate is a required parameter for the align.seqs command.");
- mothurOutEndLine();
- abort = true;
+ candidateFileName = validParameter.validFile(parameters, "candidate", false);
+ if (candidateFileName == "not found") { mothurOut("candidate is a required parameter for the align.seqs command."); mothurOutEndLine(); abort = true; }
+ else {
+ splitAtDash(candidateFileName, candidateFileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < candidateFileNames.size(); i++) {
+ if (inputDir != "") {
+ string path = hasPath(candidateFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { candidateFileNames[i] = inputDir + candidateFileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
+ ableToOpen = openInputFile(candidateFileNames[i], in);
+ if (ableToOpen == 1) {
+ mothurOut(candidateFileNames[i] + " will be disregarded."); mothurOutEndLine();
+ //erase from file list
+ candidateFileNames.erase(candidateFileNames.begin()+i);
+ i--;
+ }
+ in.close();
+ }
+
+ //make sure there is at least one valid file left
+ if (candidateFileNames.size() == 0) { mothurOut("no valid files."); mothurOutEndLine(); abort = true; }
}
- else if (candidateFileName == "not open") { abort = true; }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
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 = "0.50"; }
+ 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"; }
try {
mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
- mothurOut("The template and candidate parameters are required.\n");
+ mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
mothurOut("The search parameter allows you to specify the method to find most similar template. Your options are: suffix, kmer and blast. The default is kmer.\n");
mothurOut("The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
- mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 7.\n");
+ mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
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 gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
+ mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n");
+ mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse complement 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. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.\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 0.50, meaning at least 50% 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");
try {
if (abort == true) { return 0; }
- if(search == "kmer") { templateDB = new KmerDB(templateFileName, kmerSize); }
- else if(search == "suffix") { templateDB = new SuffixDB(templateFileName); }
- else if(search == "blast") { templateDB = new BlastDB(templateFileName, gapOpen, gapExtend, match, misMatch); }
- else {
- mothurOut(search + " is not a valid search option. I will run the command using kmer, ksize=8.");
- mothurOutEndLine();
- kmerSize = 8;
-
- templateDB = new KmerDB(templateFileName, kmerSize);
- }
-
+ templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
int longestBase = templateDB->getLongestBase();
-
+
if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
mothurOutEndLine();
alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
}
- mothurOut("Aligning sequences...");
- mothurOutEndLine();
-
- string alignFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align";
- string reportFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "align.report";
- int numFastaSeqs = 0;
- int start = time(NULL);
-
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- ifstream inFASTA;
- openInputFile(candidateFileName, inFASTA);
- numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
-
- lines.push_back(new linePair(0, numFastaSeqs));
-
- driver(lines[0], alignFileName, reportFileName);
+ for (int s = 0; s < candidateFileNames.size(); s++) {
+ mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); mothurOutEndLine();
- }
- else{
- vector<int> positions;
- processIDS.resize(0);
+ if (outputDir == "") { outputDir += hasPath(candidateFileNames[s]); }
+ string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
+ string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report";
+ string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos";
- ifstream inFASTA;
- openInputFile(candidateFileName, inFASTA);
+ int numFastaSeqs = 0;
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ int start = time(NULL);
- string input;
- while(!inFASTA.eof()){
- input = getline(inFASTA);
- if (input.length() != 0) {
- if(input[0] == '>'){ int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ openInputFile(candidateFileNames[s], inFASTA);
+ numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numFastaSeqs));
+
+ driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+
+ //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;
+ processIDS.resize(0);
+
+ ifstream inFASTA;
+ openInputFile(candidateFileNames[s], inFASTA);
+
+ string input;
+ while(!inFASTA.eof()){
+ input = getline(inFASTA);
+ if (input.length() != 0) {
+ if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ }
+ }
+ inFASTA.close();
+
+ numFastaSeqs = positions.size();
+
+ int numSeqsPerProcessor = numFastaSeqs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ long int startPos = positions[ i * numSeqsPerProcessor ];
+ if(i == processors - 1){
+ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+ }
+ lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ }
+
+ createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+
+ rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
+ rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
+
+ //append alignment and report files
+ for(int i=1;i<processors;i++){
+ appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
+ remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
+
+ appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
+ remove((reportFileName + toString(processIDS[i]) + ".temp").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();
+ }
+ }
+#else
+ ifstream inFASTA;
+ openInputFile(candidateFileNames[s], inFASTA);
+ numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
inFASTA.close();
- numFastaSeqs = positions.size();
+ lines.push_back(new linePair(0, numFastaSeqs));
- int numSeqsPerProcessor = numFastaSeqs / processors;
+ driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
- for (int i = 0; i < processors; i++) {
- int startPos = positions[ i * numSeqsPerProcessor ];
- if(i == processors - 1){
- numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
- }
- lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ //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();
}
- createProcesses(alignFileName, reportFileName);
- rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
- rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
+#endif
- for(int i=1;i<processors;i++){
- appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
- remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
-
- appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
- remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
- }
+
+ mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
+ mothurOutEndLine();
+ mothurOutEndLine();
}
-#else
- ifstream inFASTA;
- openInputFile(candidateFileName, inFASTA);
- numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
-
- lines.push_back(new linePair(0, numFastaSeqs));
-
- driver(lines[0], alignFileName, reportFileName);
-#endif
-
- mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
- mothurOutEndLine();
- mothurOutEndLine();
return 0;
}
//**********************************************************************************************************************
-int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
+int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName, string filename){
try {
ofstream alignmentFile;
openOutputFile(alignFName, alignmentFile);
+
+ ofstream accnosFile;
+ openOutputFile(accnosFName, accnosFile);
+
NastReport report(reportFName);
ifstream inFASTA;
- openInputFile(candidateFileName, inFASTA);
+ openInputFile(filename, inFASTA);
inFASTA.seekg(line->start);
-
+
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* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
+ int origNumBases = candidateSeq->getNumBases();
+ string originalUnaligned = candidateSeq->getUnaligned();
+ int numBasesNeeded = origNumBases * threshold;
- Sequence temp = templateDB->findClosestSequence(candidateSeq);
- Sequence* templateSeq = &temp;
-
- report.setTemplate(templateSeq);
- report.setSearchParameters(search, templateDB->getSearchScore());
-
- Nast nast(alignment, candidateSeq, templateSeq);
-
- report.setAlignmentParameters(align, alignment);
-
- report.setNastParameters(nast);
-
- alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
-
- report.print();
+ 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;
+
+ float searchScore = templateDB->getSearchScore();
+
+ Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
+ Sequence* copy;
+
+ 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;
- delete candidateSeq;
+ //report progress
+ if((i+1) % 100 == 0){ mothurOut(toString(i+1)); mothurOutEndLine(); }
}
+ //report progress
+ if((line->numSeqs) % 100 != 0){ mothurOut(toString(line->numSeqs)); mothurOutEndLine(); }
alignmentFile.close();
inFASTA.close();
+ accnosFile.close();
return 1;
}
/**************************************************************************************************/
-void AlignCommand::createProcesses(string alignFileName, string reportFileName) {
+void AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
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", filename);
exit(0);
}else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
}
exit(1);
}
}
-
-/**************************************************************************************************/
+//**********************************************************************************************************************
void AlignCommand::appendReportFiles(string temp, string filename) {
try{