#include "nast.hpp"
#include "nastreport.hpp"
+#include "referencedb.h"
//**********************************************************************************************************************
vector<string> AlignCommand::setParameters(){
CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
+ CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(pthreshold);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
string AlignCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n";
- helpString += "The align.seqs command parameters are reference, fasta, search, ksize, align, match, mismatch, gapopen, gapextend and processors.\n";
- helpString += "The reference and fasta parameters are required. You may leave fasta blank if you have a valid fasta file. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
- helpString += "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";
- helpString += "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";
- helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n";
- helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
- helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n";
- helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
- helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n";
- helpString += "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";
- helpString += "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";
- helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n";
- helpString += "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";
- helpString += "The align.seqs command should be in the following format: \n";
- helpString += "align.seqs(reference=yourTemplateFile, fasta=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n";
- helpString += "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";
- helpString += "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n";
+ helpString += "The align.seqs command reads a file containing sequences and creates an alignment file and a report file.";
+ helpString += "The align.seqs command parameters are reference, fasta, search, ksize, align, match, mismatch, gapopen, gapextend and processors.";
+ helpString += "The reference and fasta parameters are required. You may leave fasta blank if you have a valid fasta file. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta.";
+ helpString += "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.";
+ helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.";
+ helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.";
+ helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.";
+ helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.";
+ helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.";
+ helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.";
+ helpString += "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.";
+ helpString += "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.";
+ helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.";
+ helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
+ helpString += "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.";
+ helpString += "The align.seqs command should be in the following format:";
+ helpString += "align.seqs(reference=yourTemplateFile, fasta=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty)";
+ helpString += "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)";
+ helpString += "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).";
return helpString;
}
catch(exception& e) {
//**********************************************************************************************************************
AlignCommand::AlignCommand(string option) {
try {
- abort = false; calledHelp = false;
-
+ abort = false; calledHelp = false;
+ ReferenceDB* rdb = ReferenceDB::getInstance();
+
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true;}
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
}
}
- //check for required parameters
- templateFileName = validParameter.validFile(parameters, "reference", true);
-
- if (templateFileName == "not found") {
- m->mothurOut("reference is a required parameter for the align.seqs command.");
- m->mothurOutEndLine();
- abort = true;
- }else if (templateFileName == "not open") { abort = true; }
-
candidateFileName = validParameter.validFile(parameters, "fasta", false);
if (candidateFileName == "not found") {
//if there is a current fasta file, use it
for (int i = 0; i < candidateFileNames.size(); i++) {
//candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
- if (inputDir != "") {
- string path = m->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 = m->openInputFile(candidateFileNames[i], in, "noerror");
- in.close();
-
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
- m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- candidateFileNames[i] = tryPath;
+ bool ignore = false;
+ if (candidateFileNames[i] == "current") {
+ candidateFileNames[i] = m->getFastaFile();
+ if (candidateFileNames[i] != "") { m->mothurOut("Using " + candidateFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ candidateFileNames.erase(candidateFileNames.begin()+i);
+ i--;
}
}
- //if you can't open it, try output location
- if (ableToOpen == 1) {
- if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
- m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- candidateFileNames[i] = tryPath;
- }
- }
+ if (!ignore) {
-
-
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
- //erase from file list
- candidateFileNames.erase(candidateFileNames.begin()+i);
- i--;
+ if (inputDir != "") {
+ string path = m->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 = m->openInputFile(candidateFileNames[i], in, "noerror");
+ in.close();
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
+ m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ candidateFileNames[i] = tryPath;
+ }
+ }
+
+ //if you can't open it, try output location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
+ m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ candidateFileNames[i] = tryPath;
+ }
+ }
+
+
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ candidateFileNames.erase(candidateFileNames.begin()+i);
+ i--;
+ }else {
+ m->setFastaFile(candidateFileNames[i]);
+ }
}
-
}
//make sure there is at least one valid file left
temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; }
flip = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
+ save = m->isTrue(temp);
+ rdb->save = save;
+ if (save) { //clear out old references
+ rdb->clearMemory();
+ }
+
+ //this has to go after save so that if the user sets save=t and provides no reference we abort
+ templateFileName = validParameter.validFile(parameters, "reference", true);
+ if (templateFileName == "not found") {
+ //check for saved reference sequences
+ if (rdb->referenceSeqs.size() != 0) {
+ templateFileName = "saved";
+ }else {
+ m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the align.seqs command.");
+ m->mothurOutEndLine();
+ abort = true;
+ }
+ }else if (templateFileName == "not open") { abort = true; }
+ else { if (save) { rdb->setSavedReference(templateFileName); } }
+
temp = validParameter.validFile(parameters, "threshold", false); if (temp == "not found"){ temp = "0.50"; }
convert(temp, threshold);
//MPI_Info info;
//MPI_File_delete(outAccnosFilename, info);
hasAccnos = false;
- remove(accnosFileName.c_str());
+ m->mothurRemove(accnosFileName);
}
}
numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
#endif
- if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; }
+ if (m->control_pressed) { m->mothurRemove(accnosFileName); m->mothurRemove(alignFileName); m->mothurRemove(reportFileName); outputTypes.clear(); return 0; }
//delete accnos file if its blank else report to user
- if (m->isBlank(accnosFileName)) { remove(accnosFileName.c_str()); hasAccnos = false; }
+ if (m->isBlank(accnosFileName)) { m->mothurRemove(accnosFileName); hasAccnos = false; }
else {
m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
if (!flip) {
vector<string> nonBlankAccnosFiles;
if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
- else { remove(accnosFName.c_str()); } //remove so other files can be renamed to it
+ else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
for (int i = 0; i < processIDS.size(); i++) {
ifstream in;
string tempFile = alignFileName + toString(processIDS[i]) + ".num.temp";
m->openInputFile(tempFile, in);
if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
- in.close(); remove(tempFile.c_str());
+ in.close(); m->mothurRemove(tempFile);
appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
- remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((alignFileName + toString(processIDS[i]) + ".temp"));
appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
- remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((reportFileName + toString(processIDS[i]) + ".temp"));
if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
- }else { remove((accnosFName + toString(processIDS[i]) + ".temp").c_str()); }
+ }else { m->mothurRemove((accnosFName + toString(processIDS[i]) + ".temp")); }
}
for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
appendAlignFiles(nonBlankAccnosFiles[h], accnosFName);
- remove(nonBlankAccnosFiles[h].c_str());
+ m->mothurRemove(nonBlankAccnosFiles[h]);
}
}else { //recreate the accnosfile if needed
ofstream out;
projects / mothur.git / blobdiff