#include "sequence.hpp"
//**********************************************************************************************************************
-vector<string> ScreenSeqsCommand::getValidParameters(){
+vector<string> ScreenSeqsCommand::setParameters(){
try {
- string Array[] = {"fasta", "start", "end", "maxambig", "maxhomop","optimize","criteria", "minlength", "maxlength",
- "name", "group", "alignreport","processors","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(palignreport);
+ CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
+ CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
+ CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
+ CommandParameter pmaxhomop("maxhomop", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxhomop);
+ CommandParameter pminlength("minlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pminlength);
+ CommandParameter pmaxlength("maxlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxlength);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pcriteria("criteria", "Number", "", "90", "", "", "",false,false); parameters.push_back(pcriteria);
+ CommandParameter poptimize("optimize", "Multiple", "none-start-end-maxambig-maxhomop-minlength-maxlength", "none", "", "", "",true,false); parameters.push_back(poptimize);
+ 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, "ScreenSeqsCommand", "getValidParameters");
+ m->errorOut(e, "ScreenSeqsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ScreenSeqsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The screen.seqs command reads a fastafile and creates .....\n";
+ helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, optimize, criteria and processors.\n";
+ helpString += "The fasta parameter is required.\n";
+ helpString += "The start parameter .... The default is -1.\n";
+ helpString += "The end parameter .... The default is -1.\n";
+ helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
+ helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
+ helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
+ helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
+ helpString += "The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n";
+ helpString += "The optimize and criteria parameters allow you set the start, end, maxabig, maxhomop, minlength and maxlength parameters relative to your set of sequences .\n";
+ helpString += "For example optimize=start-end, criteria=90, would set the start and end values to the position 90% of your sequences started and ended.\n";
+ helpString += "The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n";
+ helpString += "The screen.seqs command should be in the following format: \n";
+ helpString += "screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig, \n";
+ helpString += "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n";
+ helpString += "Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\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, "ScreenSeqsCommand", "getHelpString");
exit(1);
}
}
ScreenSeqsCommand::ScreenSeqsCommand(){
try {
abort = true; calledHelp = true;
+ setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
exit(1);
}
}
-//**********************************************************************************************************************
-vector<string> ScreenSeqsCommand::getRequiredParameters(){
- try {
- string Array[] = {"fasta"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "ScreenSeqsCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> ScreenSeqsCommand::getRequiredFiles(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "ScreenSeqsCommand", "getRequiredFiles");
- exit(1);
- }
-}
//***************************************************************************************************************
ScreenSeqsCommand::ScreenSeqsCommand(string option) {
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string AlignArray[] = {"fasta", "start", "end", "maxambig", "maxhomop","optimize","criteria", "minlength", "maxlength",
- "name", "group", "alignreport","processors","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the screen.seqs command."); m->mothurOutEndLine(); abort = true; }
+ if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " 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 if (fastafile == "not open") { abort = true; }
groupfile = validParameter.validFile(parameters, "group", true);
temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "-1"; }
convert(temp, maxLength);
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
- convert(temp, processors);
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ convert(temp, processors);
temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
- if (temp == "not found"){ temp = ""; }
- else { m->splitAtDash(temp, optimize); }
+ if (temp == "not found"){ temp = "none"; }
+ m->splitAtDash(temp, optimize);
//check for invalid optimize options
set<string> validOptimizers;
- validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
-
+ validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
for (int i = 0; i < optimize.size(); i++) {
if (validOptimizers.count(optimize[i]) == 0) {
m->mothurOut(optimize[i] + " is not a valid optimizer. Valid options are start, end, maxambig, maxhomop, minlength and maxlength."); m->mothurOutEndLine();
}
}
+ if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
+
temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){ temp = "90"; }
convert(temp, criteria);
}
exit(1);
}
}
-//**********************************************************************************************************************
-
-void ScreenSeqsCommand::help(){
- try {
- m->mothurOut("The screen.seqs command reads a fastafile and creates .....\n");
- m->mothurOut("The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, optimize, criteria and processors.\n");
- m->mothurOut("The fasta parameter is required.\n");
- m->mothurOut("The start parameter .... The default is -1.\n");
- m->mothurOut("The end parameter .... The default is -1.\n");
- m->mothurOut("The maxambig parameter .... The default is -1.\n");
- m->mothurOut("The maxhomop parameter .... The default is -1.\n");
- m->mothurOut("The minlength parameter .... The default is -1.\n");
- m->mothurOut("The maxlength parameter .... The default is -1.\n");
- m->mothurOut("The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n");
- m->mothurOut("The optimize and criteria parameters allow you set the start, end, maxabig, maxhomop, minlength and maxlength parameters relative to your set of sequences .\n");
- m->mothurOut("For example optimize=start-end, criteria=90, would set the start and end values to the position 90% of your sequences started and ended.\n");
- m->mothurOut("The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n");
- m->mothurOut("The screen.seqs command should be in the following format: \n");
- m->mothurOut("screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig, \n");
- m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength) \n");
- m->mothurOut("Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\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, "ScreenSeqsCommand", "help");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-
-ScreenSeqsCommand::~ScreenSeqsCommand(){ /* do nothing */ }
-
//***************************************************************************************************************
int ScreenSeqsCommand::execute(){
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