X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=aligncommand.cpp;h=f757a7920bb337883a2a7773f35ed533d2186c80;hp=efc8ce489e79ac5e1d17084f5e952b39590894ba;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d diff --git a/aligncommand.cpp b/aligncommand.cpp index efc8ce4..f757a79 100644 --- a/aligncommand.cpp +++ b/aligncommand.cpp @@ -20,21 +20,21 @@ //********************************************************************************************************************** vector AlignCommand::setParameters(){ try { - 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 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); + CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate); + CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none","fasta-alignreport-accnos",false,true,true); parameters.push_back(pcandidate); + CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "","",false,false,true); 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,true); parameters.push_back(palign); + CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch); + CommandParameter pgapopen("gapopen", "Number", "", "-5.0", "", "", "","",false,false); parameters.push_back(pgapopen); + CommandParameter pgapextend("gapextend", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapextend); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); 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); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -57,8 +57,8 @@ string AlignCommand::getHelpString(){ 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 gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -5.0."; + helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -2.0."; 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."; @@ -76,28 +76,22 @@ string AlignCommand::getHelpString(){ } } //********************************************************************************************************************** -string AlignCommand::getOutputFileNameTag(string type, string inputName=""){ - try { - string tag = ""; - map >::iterator it; +string AlignCommand::getOutputPattern(string type) { + try { + string pattern = ""; - //is this a type this command creates - it = outputTypes.find(type); - if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } - else { - if (type == "fasta") { tag = "align"; } - else if (type == "alignreport") { tag = "align.report"; } - else if (type == "accnos") { tag = "flip.accnos"; } - else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } - } - return tag; - } - catch(exception& e) { - m->errorOut(e, "AlignCommand", "getOutputFileName"); - exit(1); - } + if (type == "fasta") { pattern = "[filename],align"; } //makes file like: amazon.align + else if (type == "alignreport") { pattern = "[filename],align.report"; } + else if (type == "accnos") { pattern = "[filename],flip.accnos"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "AlignCommand", "getOutputPattern"); + exit(1); + } } - //********************************************************************************************************************** AlignCommand::AlignCommand(){ try { @@ -255,10 +249,10 @@ AlignCommand::AlignCommand(string option) { temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; } m->mothurConvert(temp, misMatch); - temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; } + temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-5.0"; } m->mothurConvert(temp, gapOpen); - temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; } + temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-2.0"; } m->mothurConvert(temp, gapExtend); temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } @@ -328,9 +322,11 @@ int AlignCommand::execute(){ m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine(); if (outputDir == "") { outputDir += m->hasPath(candidateFileNames[s]); } - string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("fasta"); - string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("alignreport"); - string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("accnos"); + map variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])); + string alignFileName = getOutputFileName("fasta", variables); + string reportFileName = getOutputFileName("alignreport", variables); + string accnosFileName = getOutputFileName("accnos", variables); + bool hasAccnos = true; int numFastaSeqs = 0; @@ -562,6 +558,7 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam if (m->control_pressed) { break; } Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA); + cout << candidateSeq->getAligned() << endl; report.setCandidate(candidateSeq); int origNumBases = candidateSeq->getNumBases(); @@ -648,11 +645,11 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam #endif //report progress - if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } + if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count) + "\n"); } } //report progress - if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } + if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count) + "\n"); } delete alignment; alignmentFile.close(); @@ -969,6 +966,9 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s //Close all thread handles and free memory allocations. for(int i=0; i < pDataArray.size(); i++){ + if (pDataArray[i]->count != pDataArray[i]->end) { + m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; + } num += pDataArray[i]->count; CloseHandle(hThreadArray[i]); delete pDataArray[i];