#include "countseqscommand.h"
#include "groupmap.h"
#include "sharedutilities.h"
+#include "counttable.h"
//**********************************************************************************************************************
vector<string> CountSeqsCommand::setParameters(){
try {
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
- 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 pname("name", "InputTypes", "", "", "none", "none", "none","count",false,true,true); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
+ 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 CountSeqsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The count.seqs aka. make.table command reads a name file and outputs a .count.table file. You may also provide a group file to get the counts broken down by group.\n";
+ helpString += "The count.seqs aka. make.table command reads a name file and outputs a .count_table file. You may also provide a group file to get the counts broken down by group.\n";
helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
helpString += "The large parameter indicates the name and group files are too large to fit in RAM.\n";
helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
}
}
//**********************************************************************************************************************
-string CountSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string CountSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "counttable") { outputFileName = "count.table"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "CountSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "count") { pattern = "[filename],count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
CountSeqsCommand::CountSeqsCommand(){
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["counttable"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "CountSeqsCommand", "CountSeqsCommand");
//initialize outputTypes
vector<string> tempOutNames;
- outputTypes["counttable"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("counttable");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile));
+ string outputFileName = getOutputFileName("count", variables);
int total = 0;
if (!large) { total = processSmall(outputFileName); }
else { total = processLarge(outputFileName); }
-
+
if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
//set rabund file as new current rabundfile
- itTypes = outputTypes.find("counttable");
+ itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { string current = (itTypes->second)[0]; m->setCountTableFile(current); }
}
m->mothurOutEndLine();
m->mothurOut("Total number of sequences: " + toString(total)); m->mothurOutEndLine();
m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outputFileName); m->mothurOutEndLine();
m->mothurOutEndLine();
int CountSeqsCommand::processSmall(string outputFileName){
try {
ofstream out;
- m->openOutputFile(outputFileName, out); outputTypes["counttable"].push_back(outputFileName);
- outputNames.push_back(outputFileName); outputTypes["counttable"].push_back(outputFileName);
+ m->openOutputFile(outputFileName, out); outputTypes["count"].push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName);
out << "Representative_Sequence\ttotal\t";
GroupMap* groupMap;
string firstCol, secondCol;
in >> firstCol; m->gobble(in); in >> secondCol; m->gobble(in);
-
+ //cout << firstCol << '\t' << secondCol << endl;
+ m->checkName(firstCol);
+ m->checkName(secondCol);
+ //cout << firstCol << '\t' << secondCol << endl;
+
vector<string> names;
m->splitAtChar(secondCol, names, ',');
for (set<string>::iterator it = namesOfGroups.begin(); it != namesOfGroups.end(); it++) { initial[(*it)] = 0; }
ofstream out;
m->openOutputFile(outputFileName, out);
- outputNames.push_back(outputFileName); outputTypes["counttable"].push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName);
out << "Representative_Sequence\ttotal\t";
if (groupfile == "") { out << endl; }
else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
if (pairDone) {
+ m->checkName(firstCol);
+ m->checkName(secondCol);
//parse names into vector
vector<string> theseNames;
m->splitAtComma(secondCol, theseNames);
in.close();
out.close();
+ if (rest != "") {
+ vector<string> pieces = m->splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ m->checkName(firstCol);
+ m->checkName(secondCol);
+ //parse names into vector
+ vector<string> theseNames;
+ m->splitAtComma(secondCol, theseNames);
+ for (int i = 0; i < theseNames.size(); i++) { out << theseNames[i] << '\t' << count << endl; }
+ indexToNames[count] = firstCol;
+ pairDone = false;
+ count++;
+ }
+ }
+
+ }
+
return indexToNames;
}
catch(exception& e) {
else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
if (pairDone) {
+ m->checkName(firstCol);
it = groupIndex.find(secondCol);
if (it == groupIndex.end()) { //add group, assigning the group and number so we can use vectors above
groupIndex[secondCol] = count;
}
in.close();
out.close();
+
+ if (rest != "") {
+ vector<string> pieces = m->splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { firstCol = pieces[i]; columnOne=false; }
+ else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ m->checkName(firstCol);
+ it = groupIndex.find(secondCol);
+ if (it == groupIndex.end()) { //add group, assigning the group and number so we can use vectors above
+ groupIndex[secondCol] = count;
+ count++;
+ }
+ out << firstCol << '\t' << groupIndex[secondCol] << endl;
+ namesOfGroups.insert(secondCol);
+ pairDone = false;
+ }
+ }
+ }
for (it = groupIndex.begin(); it != groupIndex.end(); it++) { indexToGroups[it->second] = it->first; }
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