X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=60a1dc2f7c93818450cc60e839e91fdd9aac3fa4;hb=643cdf74ccd4fc2d565168716fb5645917dee834;hp=7bed27f7725f78425a3c2e8f61f528b24b00c830;hpb=85bf2e965f12d609c751763883b2224e6951eeba;p=mothur.git diff --git a/aligncommand.cpp b/aligncommand.cpp index 7bed27f..60a1dc2 100644 --- a/aligncommand.cpp +++ b/aligncommand.cpp @@ -25,39 +25,59 @@ #include "nast.hpp" #include "nastreport.hpp" - -//********************************************************************************************************************** -vector AlignCommand::getValidParameters(){ - try { - string AlignArray[] = {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "AlignCommand", "getValidParameters"); - exit(1); - } -} //********************************************************************************************************************** -vector AlignCommand::getRequiredParameters(){ +vector AlignCommand::setParameters(){ try { - string AlignArray[] = {"template","candidate"}; - vector 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 myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; } catch(exception& e) { - m->errorOut(e, "AlignCommand", "getRequiredParameters"); + m->errorOut(e, "AlignCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector AlignCommand::getRequiredFiles(){ +string AlignCommand::getHelpString(){ try { - vector myArray; - 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", "getRequiredFiles"); + m->errorOut(e, "AlignCommand", "getHelpString"); exit(1); } } @@ -65,6 +85,7 @@ vector AlignCommand::getRequiredFiles(){ AlignCommand::AlignCommand(){ try { abort = true; calledHelp = true; + setParameters(); vector tempOutNames; outputTypes["fasta"] = tempOutNames; outputTypes["alignreport"] = tempOutNames; @@ -84,10 +105,7 @@ AlignCommand::AlignCommand(string option) { if(option == "help") { help(); 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 myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -117,28 +135,32 @@ AlignCommand::AlignCommand(string option) { 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); - if (candidateFileName == "not found") { m->mothurOut("candidate is a required parameter for the align.seqs command."); m->mothurOutEndLine(); abort = true; } - else { + candidateFileName = validParameter.validFile(parameters, "fasta", false); + if (candidateFileName == "not found") { + //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); //go through files and make sure they are good, if not, then disregard them @@ -168,7 +190,7 @@ AlignCommand::AlignCommand(string option) { } } - //if you can't open it, try default location + //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]); @@ -213,7 +235,8 @@ AlignCommand::AlignCommand(string option) { 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"; } @@ -223,8 +246,11 @@ AlignCommand::AlignCommand(string option) { 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; } + } } @@ -234,7 +260,6 @@ AlignCommand::AlignCommand(string option) { } } //********************************************************************************************************************** - AlignCommand::~AlignCommand(){ if (abort == false) { @@ -243,37 +268,6 @@ AlignCommand::~AlignCommand(){ 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(){ @@ -463,6 +457,12 @@ int AlignCommand::execute(){ m->mothurOutEndLine(); } + //set align file as new current fastafile + string currentFasta = ""; + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); } + } m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); @@ -809,7 +809,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename); //force parent to wait until all the processes are done - for (int i=0;i