#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 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 command reads a name file and outputs a .seq.count 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";
helpString += "The count.seqs command should be in the following format: count.seqs(name=yourNameFile).\n";
- helpString += "Example count.seqs(name=amazon.names).\n";
+ helpString += "Example count.seqs(name=amazon.names) or make.table(name=amazon.names).\n";
helpString += "Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourNameFile).\n";
return helpString;
}
exit(1);
}
}
-
+//**********************************************************************************************************************
+string CountSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ 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(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
- outputTypes["summary"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "CountSeqsCommand", "CountSeqsCommand");
//initialize outputTypes
vector<string> tempOutNames;
- outputTypes["summary"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = "all"; }
m->splitAtDash(groups, Groups);
+
+ string temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "F"; }
+ large = m->isTrue(temp);
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(namefile); }
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- ofstream out;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "seq.count";
- m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName);
- out << "Representative_Sequence\ttotal\t";
+ 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("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 Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOutEndLine();
- GroupMap* groupMap;
+ return 0;
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int CountSeqsCommand::processSmall(string outputFileName){
+ try {
+ ofstream out;
+ 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;
if (groupfile != "") {
groupMap = new GroupMap(groupfile); groupMap->readMap();
if (m->control_pressed) { break; }
string firstCol, secondCol;
- in >> firstCol >> secondCol; m->gobble(in);
-
+ 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, ',');
total += names.size();
}
in.close();
+ out.close();
if (groupfile != "") { delete groupMap; }
+
+ return total;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "processSmall");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int CountSeqsCommand::processLarge(string outputFileName){
+ try {
+ set<string> namesOfGroups;
+ map<string, int> initial;
+ 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["count"].push_back(outputFileName);
+ out << "Representative_Sequence\ttotal\t";
+ if (groupfile == "") { out << endl; }
+
+ map<string, unsigned long long> namesToIndex;
+ string outfile = m->getRootName(groupfile) + "sorted.groups.temp";
+ string outName = m->getRootName(namefile) + "sorted.name.temp";
+ map<int, string> indexToName;
+ map<int, string> indexToGroup;
+ if (groupfile != "") {
+ time_t estart = time(NULL);
+ //convert name file to redundant -> unique. set unique name equal to index so we can use vectors, save name for later.
+ string newNameFile = m->getRootName(namefile) + ".name.temp";
+ string newGroupFile = m->getRootName(groupfile) + ".group.temp";
+ indexToName = processNameFile(newNameFile);
+ indexToGroup = getGroupNames(newGroupFile, namesOfGroups);
+
+ //sort file by first column so the names of sequences will be easier to find
+ //use the unix sort
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ string command = "sort -n " + newGroupFile + " -o " + outfile;
+ system(command.c_str());
+ command = "sort -n " + newNameFile + " -o " + outName;
+ system(command.c_str());
+ #else //sort using windows sort
+ string command = "sort " + newGroupFile + " /O " + outfile;
+ system(command.c_str());
+ command = "sort " + newNameFile + " /O " + outName;
+ system(command.c_str());
+ #endif
+ m->mothurRemove(newNameFile);
+ m->mothurRemove(newGroupFile);
+
+ m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort and index the group and name files. "); m->mothurOutEndLine();
+ }else { outName = namefile; }
+
+ time_t estart = time(NULL);
+ //open input file
+ ifstream in;
+ m->openInputFile(outName, in);
+
+ //open input file
+ ifstream in2;
- if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
+ int total = 0;
+ vector< vector<int> > nameMapCount;
+ if (groupfile != "") {
+ m->openInputFile(outfile, in2);
+ nameMapCount.resize(indexToName.size());
+ for (int i = 0; i < nameMapCount.size(); i++) {
+ nameMapCount[i].resize(indexToGroup.size(), 0);
+ }
+ }
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ string firstCol;
+ in >> firstCol; m->gobble(in);
+
+ if (groupfile != "") {
+ int uniqueIndex;
+ in >> uniqueIndex; m->gobble(in);
+
+ string name; int groupIndex;
+ in2 >> name >> groupIndex; m->gobble(in2);
+
+ if (name != firstCol) { m->mothurOut("[ERROR]: found " + name + " in your groupfile, but " + firstCol + " was in your namefile, please correct.\n"); m->control_pressed = true; }
+
+ nameMapCount[uniqueIndex][groupIndex]++;
+ total++;
+ }else {
+ string secondCol;
+ in >> secondCol; m->gobble(in);
+ int num = m->getNumNames(secondCol);
+ out << firstCol << '\t' << num << endl;
+ total += num;
+ }
+ }
+ in.close();
+
+ if (groupfile != "") {
+ m->mothurRemove(outfile);
+ m->mothurRemove(outName);
+ in2.close();
+ for (map<int, string>::iterator it = indexToGroup.begin(); it != indexToGroup.end(); it++) { out << it->second << '\t'; }
+ out << endl;
+ for (int i = 0; i < nameMapCount.size(); i++) {
+ string totalsLine = "";
+ int seqTotal = 0;
+ for (int j = 0; j < nameMapCount[i].size(); j++) {
+ seqTotal += nameMapCount[i][j];
+ totalsLine += toString(nameMapCount[i][j]) + '\t';
+ }
+ out << indexToName[i] << '\t' << seqTotal << '\t' << totalsLine << endl;
+ }
+ }
+
+ out.close();
+
+ m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to create the count table file. "); m->mothurOutEndLine();
+
+ return total;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountSeqsCommand", "processLarge");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+map<int, string> CountSeqsCommand::processNameFile(string name) {
+ try {
+ map<int, string> indexToNames;
+
+ ofstream out;
+ m->openOutputFile(name, out);
+
+ //open input file
+ ifstream in;
+ m->openInputFile(namefile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+ int count = 0;
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = m->splitWhiteSpace(rest, buffer, in.gcount());
+
+ 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++;
+ }
+ }
+ }
+ in.close();
+ out.close();
- m->mothurOutEndLine();
- m->mothurOut("Total number of sequences: " + toString(total)); m->mothurOutEndLine();
- m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine();
- m->mothurOutEndLine();
+ 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) {
+ m->errorOut(e, "CountSeqsCommand", "processNameFile");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+map<int, string> CountSeqsCommand::getGroupNames(string filename, set<string>& namesOfGroups) {
+ try {
+ map<int, string> indexToGroups;
+ map<string, int> groupIndex;
+ map<string, int>::iterator it;
+
+ ofstream out;
+ m->openOutputFile(filename, out);
+
+ //open input file
+ ifstream in;
+ m->openInputFile(groupfile, in);
+
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+ string firstCol, secondCol;
+ int count = 0;
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ in.read(buffer, 4096);
+ vector<string> pieces = m->splitWhiteSpace(rest, buffer, in.gcount());
+
+ 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;
+ }
+ }
+ }
+ 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;
+ }
+ }
+ }
- return 0;
+ for (it = groupIndex.begin(); it != groupIndex.end(); it++) { indexToGroups[it->second] = it->first; }
+
+ return indexToGroups;
}
-
catch(exception& e) {
- m->errorOut(e, "CountSeqsCommand", "execute");
+ m->errorOut(e, "CountSeqsCommand", "getGroupNames");
exit(1);
}
}
//**********************************************************************************************************************
+
+
+
projects / mothur.git / blobdiff