}
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++) {
+ 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...
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 8.\n");
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";
- string accnosFileName = candidateFileName.substr(0,candidateFileName.find_last_of(".")+1) + "flip.accnos";
-
- int numFastaSeqs = 0;
- int start = time(NULL);
+ for (int s = 0; s < candidateFileNames.size(); s++) {
+ mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); mothurOutEndLine();
+
+ string alignFileName = candidateFileNames[s].substr(0,candidateFileNames[s].find_last_of(".")+1) + "align";
+ string reportFileName = candidateFileNames[s].substr(0,candidateFileNames[s].find_last_of(".")+1) + "align.report";
+ string accnosFileName = candidateFileNames[s].substr(0,candidateFileNames[s].find_last_of(".")+1) + "flip.accnos";
+
+ int numFastaSeqs = 0;
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ int start = time(NULL);
+
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
+ 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(candidateFileName, inFASTA);
+ openInputFile(candidateFileName[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);
//delete accnos file if its blank else report to user
}else{ mothurOut(" If the reverse compliment proved to be better it was reported."); }
mothurOutEndLine();
}
- }
- else{
- vector<int> positions;
- processIDS.resize(0);
-
- ifstream inFASTA;
- openInputFile(candidateFileName, 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);
-
- rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
- rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
+#endif
- //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(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, 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."); }
+ mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
+ mothurOutEndLine();
mothurOutEndLine();
}
-#endif
-
-
-
- mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
- mothurOutEndLine();
- mothurOutEndLine();
-
return 0;
}
catch(exception& e) {
//**********************************************************************************************************************
-int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName){
+int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName, string filename){
try {
ofstream alignmentFile;
openOutputFile(alignFName, alignmentFile);
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); gobble(inFASTA);
int origNumBases = candidateSeq->getNumBases();
string originalUnaligned = candidateSeq->getUnaligned();
//report progress
if((i+1) % 100 == 0){ mothurOut(toString(i+1)); mothurOutEndLine(); }
-
}
//report progress
if((line->numSeqs) % 100 != 0){ mothurOut(toString(line->numSeqs)); mothurOutEndLine(); }
/**************************************************************************************************/
-void AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName) {
+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", accnosFName + 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); }
}