#include "pintail.h"
#include "ccode.h"
#include "chimeracheckrdp.h"
+#include "chimeraslayer.h"
//***************************************************************************************************************
else {
//valid paramters for this command
- string Array[] = {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name" };
+ string Array[] = {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents", "iters","outputdir","inputdir" };
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string,string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("template");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["template"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("conservation");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["conservation"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("quantile");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["quantile"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+ }
+
+
//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; }
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
+ }
+
templatefile = validParameter.validFile(parameters, "template", true);
if (templatefile == "not open") { abort = true; }
else if (templatefile == "not found") { templatefile = ""; }
maskfile = validParameter.validFile(parameters, "mask", false);
if (maskfile == "not found") { maskfile = ""; }
else if (maskfile != "default") {
+ if (inputDir != "") {
+ string path = hasPath(maskfile);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { maskfile = inputDir + maskfile; }
+ }
+
ifstream in;
int ableToOpen = openInputFile(maskfile, in);
if (ableToOpen == 1) { abort = true; }
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"; }
+ 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")) { temp = "10"; }
+ 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") { temp = "20"; }
+ 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 or chimeracheck methods."); mothurOutEndLine(); abort = true; }
+ if (((method != "bellerophon")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail, ccode, chimeraslayer or chimeracheck methods."); mothurOutEndLine(); abort = true; }
}
//"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 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 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=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");
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); }
+ if (method == "bellerophon") { chimera = new Bellerophon(fastafile, outputDir); }
+ else if (method == "pintail") { chimera = new Pintail(fastafile, templatefile, outputDir); }
+ else if (method == "ccode") { chimera = new Ccode(fastafile, templatefile, outputDir); }
+ else if (method == "chimeracheck") { chimera = new ChimeraCheckRDP(fastafile, templatefile, outputDir); }
+ else if (method == "chimeraslayer") { chimera = new ChimeraSlayer(fastafile, templatefile); }
else { mothurOut("Not a valid method."); mothurOutEndLine(); return 0; }
//set user options
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
- chimera->getChimeras();
+ int error = chimera->getChimeras();
- string outputFileName = getRootName(fastafile) + method + maskfile + ".chimeras";
+ //there was a problem
+ if (error == 1) { return 0; }
+
+ string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + method + maskfile + ".chimeras";
ofstream out;
openOutputFile(outputFileName, out);
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