X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;h=a422c8883ea9f172fe076961fa7705cb548e767e;hb=15dfbabd5aa00c468a43f1f99cb73b2ebc5b5e3f;hp=9299f897657c993e92707216f03ec3e8590ec7f2;hpb=e73e95146e342e952ff96efbd67677bec2120e83;p=mothur.git diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp index 9299f89..a422c88 100644 --- a/chimeraslayercommand.cpp +++ b/chimeraslayercommand.cpp @@ -23,15 +23,15 @@ vector ChimeraSlayerCommand::setParameters(){ CommandParameter pmismatch("mismatch", "Number", "", "-4.0", "", "", "",false,false); parameters.push_back(pmismatch); CommandParameter pminsim("minsim", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminsim); CommandParameter pmincov("mincov", "Number", "", "70", "", "", "",false,false); parameters.push_back(pmincov); - CommandParameter pminsnp("minsnp", "Number", "", "100", "", "", "",false,false); parameters.push_back(pminsnp); + CommandParameter pminsnp("minsnp", "Number", "", "10", "", "", "",false,false); parameters.push_back(pminsnp); CommandParameter pminbs("minbs", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminbs); - CommandParameter psearch("search", "Multiple", "kmer-blast-distance", "distance", "", "", "",false,false); parameters.push_back(psearch); + CommandParameter psearch("search", "Multiple", "kmer-blast", "blast", "", "", "",false,false); parameters.push_back(psearch); CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); CommandParameter prealign("realign", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(prealign); CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptrim); CommandParameter psplit("split", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psplit); CommandParameter pnumwanted("numwanted", "Number", "", "15", "", "", "",false,false); parameters.push_back(pnumwanted); - CommandParameter piters("iters", "Number", "", "100", "", "", "",false,false); parameters.push_back(piters); + CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters); CommandParameter pdivergence("divergence", "Number", "", "1.007", "", "", "",false,false); parameters.push_back(pdivergence); CommandParameter pparents("parents", "Number", "", "3", "", "", "",false,false); parameters.push_back(pparents); CommandParameter pincrement("increment", "Number", "", "5", "", "", "",false,false); parameters.push_back(pincrement); @@ -72,12 +72,12 @@ string ChimeraSlayerCommand::getHelpString(){ helpString += "The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3. \n"; helpString += "The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n"; helpString += "The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n"; - helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n"; + helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=1000.\n"; helpString += "The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n"; helpString += "The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n"; helpString += "The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n"; - helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 100) \n"; - helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n"; + helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n"; + helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are blast, and kmer, default blast. \n"; helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default true. \n"; helpString += "The chimera.slayer command should be in the following format: \n"; helpString += "chimera.slayer(fasta=yourFastaFile, reference=yourTemplate, search=yourSearch) \n"; @@ -112,6 +112,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { vector myArray = setParameters(); @@ -304,9 +305,10 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { templatefile = validParameter.validFile(parameters, "reference", true); if (templatefile == "not open") { abort = true; } - else if (templatefile == "not found") { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; } + else if (templatefile == "not found") { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.slayer command, unless and namefile is given."); m->mothurOutEndLine(); abort = true; } } - } + }else if (hasName) { templatefile = "self"; } + else { templatefile = ""; m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true; } string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } m->setProcessors(temp); @@ -351,9 +353,9 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { temp = validParameter.validFile(parameters, "split", false); if (temp == "not found") { temp = "f"; } trimera = m->isTrue(temp); - search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "distance"; } + search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "blast"; } - temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; } + temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } convert(temp, iters); temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "5"; } @@ -362,7 +364,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option) { temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "15"; } convert(temp, numwanted); - if ((search != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true; } + if ((search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true; } } } catch(exception& e) { @@ -732,7 +734,6 @@ int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string f #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) unsigned long int pos = inFASTA.tellg(); - //cout << candidateSeq->getName() << '\t' << pos << endl; if ((pos == -1) || (pos >= filePos->end)) { break; } #else if (inFASTA.eof()) { break; }