X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraseqscommand.cpp;h=9013e7d33f66f38b7ce1283ee92a45be3d4ab76c;hb=d9b668f68b99f92ecdc71dd8cd363cb4e27107f9;hp=3632e6363b2414eb67b1d90fd958175f7f0bc8aa;hpb=a5afca18544555fba2d9c3670ad1f8574916b0a0;p=mothur.git diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp index 3632e63..9013e7d 100644 --- a/chimeraseqscommand.cpp +++ b/chimeraseqscommand.cpp @@ -8,178 +8,46 @@ */ #include "chimeraseqscommand.h" -#include "bellerophon.h" -#include "pintail.h" -#include "ccode.h" -#include "chimeracheckrdp.h" -#include "chimeraslayer.h" - -//*************************************************************************************************************** - -ChimeraSeqsCommand::ChimeraSeqsCommand(string option){ +//********************************************************************************************************************** +vector ChimeraSeqsCommand::getValidParameters(){ try { - abort = false; - - //allow user to run help - if(option == "help") { help(); abort = true; } - - else { - //valid paramters for this command - string Array[] = {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents", "iters" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - - OptionParser parser(option); - map parameters = parser.getParameters(); - - ValidParameters validParameter; - - //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { - if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } - } - - //check for required parameters - fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = true; } - else if (fastafile == "not found") { fastafile = ""; mothurOut("fasta is a required parameter for the chimera.seqs command."); mothurOutEndLine(); abort = true; } - - templatefile = validParameter.validFile(parameters, "template", true); - if (templatefile == "not open") { abort = true; } - else if (templatefile == "not found") { templatefile = ""; } - - consfile = validParameter.validFile(parameters, "conservation", true); - if (consfile == "not open") { abort = true; } - else if (consfile == "not found") { consfile = ""; } - - quanfile = validParameter.validFile(parameters, "quantile", true); - if (quanfile == "not open") { abort = true; } - else if (quanfile == "not found") { quanfile = ""; } - - namefile = validParameter.validFile(parameters, "name", true); - if (namefile == "not open") { abort = true; } - else if (namefile == "not found") { namefile = ""; } - - maskfile = validParameter.validFile(parameters, "mask", false); - if (maskfile == "not found") { maskfile = ""; } - else if (maskfile != "default") { - ifstream in; - int ableToOpen = openInputFile(maskfile, in); - if (ableToOpen == 1) { abort = true; } - in.close(); - } - - method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "pintail"; } - - string temp; - temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; } - filter = isTrue(temp); - - temp = validParameter.validFile(parameters, "correction", false); if (temp == "not found") { temp = "T"; } - correction = isTrue(temp); - - temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; } - convert(temp, processors); - - temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; } - convert(temp, ksize); - - temp = validParameter.validFile(parameters, "svg", false); if (temp == "not found") { temp = "F"; } - svg = isTrue(temp); - - temp = validParameter.validFile(parameters, "window", false); - if ((temp == "not found") && (method == "chimeraslayer")) { temp = "100"; } - else if (temp == "not found") { temp = "0"; } - convert(temp, window); - - temp = validParameter.validFile(parameters, "match", false); if (temp == "not found") { temp = "5"; } - convert(temp, match); - - temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found") { temp = "-4"; } - convert(temp, mismatch); - - temp = validParameter.validFile(parameters, "divergence", false); if (temp == "not found") { temp = "1.0"; } - convert(temp, divR); - - temp = validParameter.validFile(parameters, "minsim", false); if (temp == "not found") { temp = "90"; } - convert(temp, minSimilarity); - - temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "5"; } - convert(temp, parents); - - 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") && ((method == "chimeracheck") || (method == "chimeraslayer"))) { temp = "10"; } - else if (temp == "not found") { temp = "25"; } - convert(temp, increment); - - temp = validParameter.validFile(parameters, "numwanted", false); - if ((temp == "not found") && (method == "chimeraslayer")) { temp = "10"; } - else if (temp == "not found") { temp = "20"; } - convert(temp, numwanted); - - - - if (((method != "bellerophon")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail, ccode, chimeraslayer or chimeracheck methods."); mothurOutEndLine(); abort = true; } - - - } + vector myArray; + return myArray; } catch(exception& e) { - errorOut(e, "ChimeraSeqsCommand", "ChimeraSeqsCommand"); + m->errorOut(e, "ChimeraSeqsCommand", "getValidParameters"); exit(1); } } //********************************************************************************************************************** - -void ChimeraSeqsCommand::help(){ +vector ChimeraSeqsCommand::getRequiredParameters(){ try { - - //"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name" - //mothurOut("chimera.seqs ASSUMES that your sequences are ALIGNED and if using a template that the template file sequences are the same length as the fasta file sequences.\n\n"); - mothurOut("The chimera.seqs command reads a fastafile and creates list of potentially chimeric sequences.\n"); - mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors, mask, method, window, increment, template, conservation, quantile, numwanted, ksize, svg, name, iters.\n"); - mothurOut("The fasta parameter is always required and template is required if using pintail, ccode or chimeracheck.\n"); - mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n"); - mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs.\n"); - mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n"); - mothurOut("The method parameter allows you to specify the method for finding chimeric sequences. The default is pintail. Options include bellerophon, ccode and chimeracheck \n"); - mothurOut("The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n"); - mothurOut("The window parameter allows you to specify the window size for searching for chimeras. \n"); - mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences.\n"); - mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences. \n"); - mothurOut("The conservation parameter allows you to enter a frequency file containing the highest bases frequency at each place in the alignment.\n"); - mothurOut("The quantile parameter allows you to enter a file containing quantiles for a template files sequences.\n"); - mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n"); - mothurOut("The ksize parameter allows you to input kmersize. \n"); - mothurOut("The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence.\n"); - mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n"); - //mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method.\n"); - mothurOut("NOT ALL PARAMETERS ARE USED BY ALL METHODS. Please look below for method specifics.\n\n"); - mothurOut("Details for each method: \n"); - mothurOut("\tpintail: \n"); - mothurOut("\t\tparameters: fasta=required, template=required, filter=F, mask=no mask, processors=1, window=300, increment=25, conservation=not required, but will improve speed, quantile=not required, but will greatly improve speed. \n"); - mothurOut("\t\tIf you have run chimera.seqs using pintail a .quan and .freq file will be created for your template, if you have not provided them for use in future command executions.\n"); - mothurOut("\tbellerophon: \n"); - mothurOut("\t\tparameters: fasta=required, filter=F, processors=1, window=1/4 length of seq, increment=25, correction=T. \n"); - mothurOut("\tccode: \n"); - mothurOut("\t\tparameters: fasta=required, template=required, filter=F, mask=no mask, processors=1, window=10% of length, numwanted=20\n"); - mothurOut("\tchimeracheck: \n"); - mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, ksize=7, svg=F, name=none\n\n"); - //mothurOut("\tchimeraslayer: \n"); - //mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, mask=no mask, numwanted=10, match=5, mismatch=-4, divergence=1.0, minsim=90, parents=5, iters=1000, window=100. \n\n"); - mothurOut("The chimera.seqs command should be in the following format: \n"); - mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n"); - mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, method=bellerophon, window=200) \n"); - mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n"); + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ChimeraSeqsCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ChimeraSeqsCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; } catch(exception& e) { - errorOut(e, "ChimeraSeqsCommand", "help"); + m->errorOut(e, "ChimeraSeqsCommand", "getRequiredFiles"); exit(1); } } +//*************************************************************************************************************** + +ChimeraSeqsCommand::ChimeraSeqsCommand(string option) {} +//********************************************************************************************************************** + +void ChimeraSeqsCommand::help(){} //*************************************************************************************************************** @@ -188,68 +56,12 @@ ChimeraSeqsCommand::~ChimeraSeqsCommand(){ /* do nothing */ } //*************************************************************************************************************** int ChimeraSeqsCommand::execute(){ - try{ - - if (abort == true) { return 0; } - - if (method == "bellerophon") { chimera = new Bellerophon(fastafile); } - else if (method == "pintail") { chimera = new Pintail(fastafile, templatefile); } - else if (method == "ccode") { chimera = new Ccode(fastafile, templatefile); } - else if (method == "chimeracheck") { chimera = new ChimeraCheckRDP(fastafile, templatefile); } - //else if (method == "chimeraslayer") { chimera = new ChimeraSlayer(fastafile, templatefile); } - else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0; } - - //set user options - if (maskfile == "default") { mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); mothurOutEndLine(); } - - //saves time to avoid generating it - chimera->setCons(consfile); - - //saves time to avoid generating it - chimera->setQuantiles(quanfile); - - chimera->setMask(maskfile); - chimera->setFilter(filter); - chimera->setCorrection(correction); - chimera->setProcessors(processors); - chimera->setWindow(window); - chimera->setIncrement(increment); - chimera->setNumWanted(numwanted); - chimera->setKmerSize(ksize); - chimera->setSVG(svg); - chimera->setName(namefile); - chimera->setMatch(match); - chimera->setMisMatch(mismatch); - chimera->setDivR(divR); - chimera->setParents(parents); - chimera->setMinSim(minSimilarity); - chimera->setIters(iters); - - - //find chimeras - int error = chimera->getChimeras(); - - //there was a problem - if (error == 1) { return 0; } - - string outputFileName = getRootName(fastafile) + method + maskfile + ".chimeras"; - ofstream out; - openOutputFile(outputFileName, out); - - //print results - chimera->print(out); - - out.close(); - - delete chimera; - - return 0; - - } - catch(exception& e) { - errorOut(e, "ChimeraSeqsCommand", "execute"); - exit(1); - } + + m->mothurOut("The chimera.seqs command has been broken up into 5 separate commands.\n"); + m->mothurOut("The chimera.bellerophon, chimera.ccode, chimera.check, chimera.pintail and chimera.slayer commands.\n"); + + return 0; } -/**************************************************************************************************/ +//********************************************************************************************************************** +