#include "nast.hpp"
#include "nastreport.hpp"
-
//**********************************************************************************************************************
-vector<string> AlignCommand::getValidParameters(){
+vector<string> AlignCommand::setParameters(){
try {
- 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)));
+ CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
+ CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcandidate);
+ CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "",false,false); parameters.push_back(psearch);
+ CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
+ CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
+ CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
+ CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
+ CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
+ 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 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);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "AlignCommand", "getValidParameters");
+ m->errorOut(e, "AlignCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> AlignCommand::getRequiredParameters(){
+string AlignCommand::getHelpString(){
try {
- string AlignArray[] = {"template","candidate"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
- return myArray;
+ string helpString = "";
+ 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 += "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) {
- m->errorOut(e, "AlignCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> AlignCommand::getRequiredFiles(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCommand", "getRequiredFiles");
+ m->errorOut(e, "AlignCommand", "getHelpString");
exit(1);
}
}
AlignCommand::AlignCommand(){
try {
abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["alignreport"] = tempOutNames;
AlignCommand::AlignCommand(string option) {
try {
abort = false; calledHelp = false;
- currentFiles = CurrentFile::getInstance();
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true;}
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
-
- //valid paramters for this command
- 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)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
else {
string path;
- it = parameters.find("template");
+ it = parameters.find("reference");
//user has given a template file
if(it != parameters.end()){
path = m->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; }
+ if (path == "") { parameters["reference"] = inputDir + it->second; }
}
}
//check for required parameters
- templateFileName = validParameter.validFile(parameters, "template", true);
+ templateFileName = validParameter.validFile(parameters, "reference", true);
if (templateFileName == "not found") {
- m->mothurOut("template is a required parameter for the align.seqs command.");
+ 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, "candidate", false);
+ candidateFileName = validParameter.validFile(parameters, "fasta", false);
if (candidateFileName == "not found") {
- //check currentFiles for a fasta file
- if (currentFiles->getFastaFile() != "") { candidateFileName = currentFiles->getFastaFile(); m->mothurOut("Using " + candidateFileName + " as candidate file."); m->mothurOutEndLine();
- }else { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true; }
+ //if there is a current fasta file, use it
+ string filename = m->getFastaFile();
+ if (filename != "") { candidateFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the candidate parameter is required."); m->mothurOutEndLine(); abort = true; }
}else {
m->splitAtDash(candidateFileName, candidateFileNames);
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 (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--;
+ 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--;
+ }
}
-
}
//make sure there is at least one valid file left
temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
convert(temp, gapExtend);
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
convert(temp, processors);
temp = validParameter.validFile(parameters, "flip", false); if (temp == "not found"){ temp = "f"; }
convert(temp, threshold);
search = validParameter.validFile(parameters, "search", false); if (search == "not found"){ search = "kmer"; }
+ if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
+ if ((align != "needleman") && (align != "gotoh") && (align != "blast") && (align != "noalign")) { m->mothurOut("invalid align option: choices are needleman, gotoh, blast or noalign."); m->mothurOutEndLine(); abort=true; }
+
}
}
}
}
//**********************************************************************************************************************
-
AlignCommand::~AlignCommand(){
if (abort == false) {
delete alignment;
}
}
-
-//**********************************************************************************************************************
-
-void AlignCommand::help(){
- try {
- m->mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
- m->mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen, gapextend and processors.\n");
- m->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");
- m->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");
- m->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");
- m->mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate. The default is 8.\n");
- m->mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
- m->mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n");
- m->mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
- m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n");
- m->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");
- m->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");
- m->mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
- m->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");
- m->mothurOut("The align.seqs command should be in the following format: \n");
- m->mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
- m->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");
- m->mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "AlignCommand", "help");
- exit(1);
- }
-}
-
-
//**********************************************************************************************************************
int AlignCommand::execute(){
string currentFasta = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; }
+ if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
}
- currentFiles->setFastaFile(currentFasta);
- cout << "current fasta = " << currentFiles->getFastaFile() << endl;
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
//force parent to wait until all the processes are done
- for (int i=0;i<processors;i++) {
+ for (int i=0;i<processIDS.size();i++) {
int temp = processIDS[i];
wait(&temp);
}
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