//**********************************************************************************************************************
vector<string> CountGroupsCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pshared);
- CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pgroup);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","summary",false,false,true); parameters.push_back(pshared);
+ CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","summary",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pcount("count", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none","summary",false,false,true); parameters.push_back(pcount);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ 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); }
}
}
//**********************************************************************************************************************
+string CountGroupsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "summary") { pattern = "[filename],count.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PrimerDesignCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
string CountGroupsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The count.groups command counts sequences from a specfic group or set of groups from the following file types: group or shared file.\n";
+ helpString += "The count.groups command counts sequences from a specific group or set of groups from the following file types: group, count or shared file.\n";
helpString += "The count.groups command parameters are accnos, group, shared and groups. You must provide a group or shared file.\n";
helpString += "The accnos parameter allows you to provide a file containing the list of groups.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n";
try {
abort = true; calledHelp = true;
setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "CountGroupsCommand", "CountGroupsCommand");
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["shared"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
}
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
//check for required parameters
accnosfile = validParameter.validFile(parameters, "accnos", true);
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
- else { m->setGroupFile(groupfile); }
+ else { m->setGroupFile(groupfile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else {
+ m->setCountTableFile(countfile);
+ CountTable ct;
+ if (!ct.testGroups(countfile)) { m->mothurOut("[ERROR]: Your count file does not have any group information, aborting."); m->mothurOutEndLine(); abort=true; }
+ }
+
+ if ((groupfile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
+ }
+
- if ((sharedfile == "") && (groupfile == "")) {
+ if ((sharedfile == "") && (groupfile == "") && (countfile == "")) {
//give priority to shared, then group
sharedfile = m->getSharedFile();
if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
groupfile = m->getGroupFile();
if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
else {
- m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
+ countfile = m->getCountTableFile();
+ if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current groupfile, countfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
+ }
}
}
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get groups you want to remove
- if (accnosfile != "") { readAccnos(); }
+ if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
if (groupfile != "") {
+ map<string, string> variables;
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ string outputFileName = getOutputFileName("summary", variables);
+ outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
GroupMap groupMap(groupfile);
groupMap.readMap();
vector<string> nameGroups = groupMap.getNamesOfGroups();
util.setGroups(Groups, nameGroups);
+ int total = 0;
for (int i = 0; i < Groups.size(); i++) {
- m->mothurOut(Groups[i] + " contains " + toString(groupMap.getNumSeqs(Groups[i])) + "."); m->mothurOutEndLine();
+ int num = groupMap.getNumSeqs(Groups[i]);
+ total += num;
+ m->mothurOut(Groups[i] + " contains " + toString(num) + "."); m->mothurOutEndLine();
+ out << Groups[i] << '\t' << num << endl;
}
+ out.close();
+ m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine();
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ if (countfile != "") {
+ map<string, string> variables;
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ string outputFileName = getOutputFileName("summary", variables);
+ outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ CountTable ct;
+ ct.readTable(countfile, true, false);
+
+ //make sure groups are valid
+ //takes care of user setting groupNames that are invalid or setting groups=all
+ SharedUtil util;
+ vector<string> nameGroups = ct.getNamesOfGroups();
+ util.setGroups(Groups, nameGroups);
+
+ int total = 0;
+ for (int i = 0; i < Groups.size(); i++) {
+ int num = ct.getGroupCount(Groups[i]);
+ total += num;
+ m->mothurOut(Groups[i] + " contains " + toString(num) + "."); m->mothurOutEndLine();
+ out << Groups[i] << '\t' << num << endl;
+ }
+ out.close();
+
+ m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine();
}
if (m->control_pressed) { return 0; }
InputData input(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
+ map<string, string> variables;
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ string outputFileName = getOutputFileName("summary", variables);
+ outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ int total = 0;
for (int i = 0; i < lookup.size(); i++) {
- m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + "."); m->mothurOutEndLine();
+ int num = lookup[i]->getNumSeqs();
+ total += num;
+ m->mothurOut(lookup[i]->getGroup() + " contains " + toString(num) + "."); m->mothurOutEndLine();
delete lookup[i];
- }
+ out << lookup[i]->getGroup() << '\t' << num << endl;
+ }
+ out.close();
+
+ m->mothurOut("\nTotal seqs: " + toString(total) + "."); m->mothurOutEndLine();
}
-
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
return 0;
}
}
}
//**********************************************************************************************************************
-void CountGroupsCommand::readAccnos(){
- try {
- Groups.clear();
-
- ifstream in;
- m->openInputFile(accnosfile, in);
- string name;
-
- while(!in.eof()){
- in >> name;
-
- Groups.push_back(name);
-
- m->gobble(in);
- }
- in.close();
-
- m->setGroups(Groups);
-
- }
- catch(exception& e) {
- m->errorOut(e, "CountGroupsCommand", "readAccnos");
- exit(1);
- }
-}
-//**********************************************************************************************************************
projects / mothur.git / blobdiff