#include "filterseqscommand.h"
#include "sequence.hpp"
+
//**********************************************************************************************************************
-vector<string> FilterSeqsCommand::getValidParameters(){
+vector<string> FilterSeqsCommand::setParameters(){
try {
- string Array[] = {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(phard);
+ CommandParameter ptrump("trump", "String", "", "*", "", "", "",false,false); parameters.push_back(ptrump);
+ CommandParameter psoft("soft", "Number", "", "0", "", "", "",false,false); parameters.push_back(psoft);
+ CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pvertical);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "FilterSeqsCommand", "getValidParameters");
+ m->errorOut(e, "FilterSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-FilterSeqsCommand::FilterSeqsCommand(){
+string FilterSeqsCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["filter"] = tempOutNames;
+ string helpString = "";
+ helpString += "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n";
+ helpString += "The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n";
+ helpString += "The fasta parameter is required, unless you have a valid current fasta file. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n";
+ helpString += "For example: fasta=abrecovery.fasta-amazon.fasta \n";
+ helpString += "The trump option will remove a column if the trump character is found at that position in any sequence of the alignment. Default=*, meaning no trump. \n";
+ helpString += "A soft mask removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences. Default=0.\n";
+ helpString += "The hard parameter allows you to enter a file containing the filter you want to use.\n";
+ helpString += "The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n";
+ helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
+ helpString += "The filter.seqs command should be in the following format: \n";
+ helpString += "filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n";
+ helpString += "Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
+ m->errorOut(e, "FilterSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> FilterSeqsCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "FilterSeqsCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> FilterSeqsCommand::getRequiredFiles(){
+FilterSeqsCommand::FilterSeqsCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["filter"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "FilterSeqsCommand", "getRequiredFiles");
+ m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
exit(1);
}
}
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for required parameters
fasta = validParameter.validFile(parameters, "fasta", false);
- if (fasta == "not found") { m->mothurOut("fasta is a required parameter for the filter.seqs command."); m->mothurOutEndLine(); abort = true; }
+ if (fasta == "not found") {
+ fasta = m->getFastaFile();
+ if (fasta != "") { fastafileNames.push_back(fasta); m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
else {
m->splitAtDash(fasta, fastafileNames);
temp = validParameter.validFile(parameters, "soft", false); if (temp == "not found") { soft = 0; }
else { soft = (float)atoi(temp.c_str()) / 100.0; }
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
convert(temp, processors);
vertical = validParameter.validFile(parameters, "vertical", false);
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void FilterSeqsCommand::help(){
- try {
-
- m->mothurOut("The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n");
- m->mothurOut("The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n");
- m->mothurOut("The fasta parameter is required. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n");
- m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
- m->mothurOut("The trump parameter .... The default is ...\n");
- m->mothurOut("The soft parameter .... The default is ....\n");
- m->mothurOut("The hard parameter allows you to enter a file containing the filter you want to use.\n");
- m->mothurOut("The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n");
- m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
- m->mothurOut("The filter.seqs command should be in the following format: \n");
- m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n");
- m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "FilterSeqsCommand", "help");
- exit(1);
- }
-}
-
/**************************************************************************************/
int FilterSeqsCommand::execute() {
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