modified sequence class to read fasta files with comments. this required modification...

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 925de63c17bf44011e9bb29e1e4b9a7a980fd3ff..bf0ffa66009ba7cdc02f46ff4d2c784e58a45a1f 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -26,7 +26,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                
                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" };
+                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents", "iters" };
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -106,6 +106,9 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        
                        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"; }
@@ -119,7 +122,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
 
                        
                        
-                       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;  }
                        
 
                }
@@ -137,7 +140,7 @@ void ChimeraSeqsCommand::help(){
                //"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");
@@ -153,6 +156,7 @@ void ChimeraSeqsCommand::help(){
                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"); 
@@ -164,6 +168,8 @@ void ChimeraSeqsCommand::help(){
                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");
@@ -217,6 +223,7 @@ int ChimeraSeqsCommand::execute(){
                chimera->setDivR(divR);
                chimera->setParents(parents);
                chimera->setMinSim(minSimilarity);
+               chimera->setIters(iters);
                
                                
                //find chimeras