X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraseqscommand.cpp;h=663b8940592f1f4ecfc8dce5ae81beadef8bef45;hb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;hp=17f3a71a5033f1d28835bbd562af5d5f9a6b5a18;hpb=fe346922fe0af5b1a025beacb211078d37598fd4;p=mothur.git diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp index 17f3a71..663b894 100644 --- a/chimeraseqscommand.cpp +++ b/chimeraseqscommand.cpp @@ -8,111 +8,13 @@ */ #include "chimeraseqscommand.h" -#include "bellerophon.h" -#include "pintail.h" //*************************************************************************************************************** -ChimeraSeqsCommand::ChimeraSeqsCommand(string option){ - 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" }; - 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 = ""; } - - 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(); - } - - - - - string temp; - temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "T"; } - 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, "window", false); if (temp == "not found") { temp = "0"; } - convert(temp, window); - - temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "25"; } - convert(temp, increment); - - method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "pintail"; } - - if ((method == "pintail") && (templatefile == "")) { mothurOut("You must provide a template file with the pintail method."); mothurOutEndLine(); abort = true; } - - - } - } - catch(exception& e) { - errorOut(e, "ChimeraSeqsCommand", "ChimeraSeqsCommand"); - exit(1); - } -} +ChimeraSeqsCommand::ChimeraSeqsCommand(string option) {} //********************************************************************************************************************** -void ChimeraSeqsCommand::help(){ - try { - mothurOut("The chimera.seqs command reads a fastafile and creates a sorted priority score list of potentially chimeric sequences (ideally, the sequences should already be aligned).\n"); - mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors, mask and method. fasta is required.\n"); - mothurOut("The filter parameter allows you to specify if you would like to apply a 50% soft filter. The default is false. \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. The default is true. \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. \n"); - mothurOut("The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the pintail and mallard method. The default is 236627 EU009184.1 Shigella dysenteriae str. FBD013. \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, processors=2, method=yourMethod) \n"); - mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n"); - } - catch(exception& e) { - errorOut(e, "ChimeraSeqsCommand", "help"); - exit(1); - } -} +void ChimeraSeqsCommand::help(){} //*************************************************************************************************************** @@ -121,53 +23,12 @@ 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); - //saves time to avoid generating it - if (consfile != "") { chimera->setCons(consfile); } - else { chimera->setCons(""); } - - //saves time to avoid generating it - if (quanfile != "") { chimera->setQuantiles(quanfile); } - else { chimera->setQuantiles(""); } - - if (maskfile == "default") { mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); mothurOutEndLine(); } - chimera->setMask(maskfile); - - }else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0; } - - //set user options - chimera->setFilter(filter); - chimera->setCorrection(correction); - chimera->setProcessors(processors); - chimera->setWindow(window); - chimera->setIncrement(increment); - - //find chimeras - chimera->getChimeras(); - - string outputFileName = getRootName(fastafile) + method + ".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; } -/**************************************************************************************************/ +//********************************************************************************************************************** +