*/
#include "chimeraseqscommand.h"
-#include "bellerophon.h"
-#include "pintail.h"
-#include "ccode.h"
-#include "chimeracheckrdp.h"
-
-//***************************************************************************************************************
-
-ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
+//**********************************************************************************************************************
+vector<string> 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" };
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
-
- ValidParameters validParameter;
-
- //check to make sure all parameters are valid for command
- for (map<string,string>::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") { temp = "0"; }
- convert(temp, window);
-
- temp = validParameter.validFile(parameters, "increment", false);
- if ((temp == "not found") && (method == "chimeracheck")) { temp = "10"; }
- else if (temp == "not found") { temp = "25"; }
- convert(temp, increment);
-
- temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "20"; }
- convert(temp, numwanted);
-
-
-
- if (((method != "bellerophon")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail, ccode or chimeracheck methods."); mothurOutEndLine(); abort = true; }
-
-
- }
+ vector<string> myArray;
+ return myArray;
}
catch(exception& e) {
- errorOut(e, "ChimeraSeqsCommand", "ChimeraSeqsCommand");
+ m->errorOut(e, "ChimeraSeqsCommand", "getValidParameters");
exit(1);
}
}
//**********************************************************************************************************************
-
-void ChimeraSeqsCommand::help(){
+vector<string> 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.\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("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("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<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSeqsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraSeqsCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
}
catch(exception& e) {
- errorOut(e, "ChimeraSeqsCommand", "help");
+ m->errorOut(e, "ChimeraSeqsCommand", "getRequiredFiles");
exit(1);
}
}
+//***************************************************************************************************************
+
+ChimeraSeqsCommand::ChimeraSeqsCommand(string option) {}
+//**********************************************************************************************************************
+
+void ChimeraSeqsCommand::help(){}
//***************************************************************************************************************
//***************************************************************************************************************
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 { 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);
-
- //find chimeras
- chimera->getChimeras();
-
- 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;
}
-/**************************************************************************************************/
+//**********************************************************************************************************************
+
projects / mothur.git / blobdiff