#include "subsamplecommand.h"
#include "sharedutilities.h"
#include "deconvolutecommand.h"
+#include "getseqscommand.h"
#include "subsample.h"
//**********************************************************************************************************************
vector<string> SubSampleCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FLSSR", "none",false,false); 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 plist("list", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(plist);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pshared);
- CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(psabund);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
- CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppersample);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FLSSR", "none","fasta",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","taxonomy",false,false,true); parameters.push_back(ptaxonomy);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FLSSR", "none","list",false,false,true); parameters.push_back(plist);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none","shared",false,false,true); parameters.push_back(pshared);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none","rabund",false,false); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none","sabund",false,false); parameters.push_back(psabund);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(psize);
+ CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(ppersample);
+ 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); }
try {
string helpString = "";
helpString += "The sub.sample command is designed to be used as a way to normalize your data, or create a smaller set from your original set.\n";
- helpString += "The sub.sample command parameters are fasta, name, list, group, rabund, sabund, shared, groups, size, persample and label. You must provide a fasta, list, sabund, rabund or shared file as an input file.\n";
+ helpString += "The sub.sample command parameters are fasta, name, list, group, count, rabund, sabund, shared, taxonomy, groups, size, persample and label. You must provide a fasta, list, sabund, rabund or shared file as an input file.\n";
helpString += "The namefile is only used with the fasta file, not with the listfile, because the list file should contain all sequences.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n";
helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
}
}
//**********************************************************************************************************************
+string SubSampleCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "sabund") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "name") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "group") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "count") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "list") { pattern = "[filename],[distance],subsample,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "shared") { pattern = "[filename],[distance],subsample,[extension]"; }
+ else if (type == "rabund") { pattern = "[filename],subsample,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSampleCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
SubSampleCommand::SubSampleCommand(){
try {
abort = true; calledHelp = true;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
+ outputTypes["taxonomy"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "SubSampleCommand", "GetRelAbundCommand");
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
+ outputTypes["taxonomy"] = tempOutNames;
//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 = ""; }
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = 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; }
+ }
+
+ it = parameters.find("taxonomy");
+ //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["taxonomy"] = inputDir + it->second; }
+ }
}
//check for required parameters
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else { m->setGroupFile(groupfile); }
+
+ taxonomyfile = validParameter.validFile(parameters, "taxonomy", true);
+ if (taxonomyfile == "not open") { taxonomyfile = ""; abort = true; }
+ else if (taxonomyfile == "not found") { taxonomyfile = ""; }
+ else { m->setTaxonomyFile(taxonomyfile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else {
+ m->setCountTableFile(countfile);
+ ct.readTable(countfile, true, false);
+ }
+
+ if ((namefile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: name or count."); 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;
+ }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
temp = validParameter.validFile(parameters, "persample", false); if (temp == "not found"){ temp = "f"; }
persample = m->isTrue(temp);
- if (groupfile == "") { persample = false; }
+ if ((groupfile == "") && (countfile == "")) { persample = false; }
+ if (countfile != "") {
+ if (!ct.hasGroupInfo()) {
+ persample = false;
+ if (pickedGroups) { m->mothurOut("You cannot pick groups without group info in your count file."); m->mothurOutEndLine(); abort = true; }
+ }
+ }
- if ((namefile != "") && (fastafile == "")) { m->mothurOut("You may only use a namefile with a fastafile."); m->mothurOutEndLine(); abort = true; }
+ if ((namefile != "") && ((fastafile == "") && (taxonomyfile == ""))) { m->mothurOut("You may only use a name file with a fasta file or taxonomy file."); m->mothurOutEndLine(); abort = true; }
+
+ if ((taxonomyfile != "") && ((fastafile == "") && (listfile == ""))) { m->mothurOut("You may only use a taxonomyfile with a fastafile or listfile."); m->mothurOutEndLine(); abort = true; }
+
if ((fastafile == "") && (listfile == "") && (sabundfile == "") && (rabundfile == "") && (sharedfile == "")) {
m->mothurOut("You must provide a fasta, list, sabund, rabund or shared file as an input file."); m->mothurOutEndLine(); abort = true; }
- if (pickedGroups && ((groupfile == "") && (sharedfile == ""))) {
- m->mothurOut("You cannot pick groups without a valid group file or shared file."); m->mothurOutEndLine(); abort = true; }
+ if (pickedGroups && ((groupfile == "") && (sharedfile == "") && (countfile == ""))) {
+ m->mothurOut("You cannot pick groups without a valid group, count or shared file."); m->mothurOutEndLine(); abort = true; }
- if ((groupfile != "") && ((fastafile == "") && (listfile == ""))) {
- m->mothurOut("Group file only valid with listfile or fastafile."); m->mothurOutEndLine(); abort = true; }
+ if (((groupfile != "") || (countfile != "")) && ((fastafile == "") && (listfile == ""))) {
+ m->mothurOut("Group or count files are only valid with listfile or fastafile."); m->mothurOutEndLine(); abort = true; }
- if ((groupfile != "") && ((fastafile != "") && (listfile != ""))) {
- m->mothurOut("A new group file can only be made from the subsample of a listfile or fastafile, not both. Please correct."); m->mothurOutEndLine(); abort = true; }
+ if (((groupfile != "") || (countfile != "")) && ((fastafile != "") && (listfile != ""))) {
+ m->mothurOut("A new group or count file can only be made from the subsample of a listfile or fastafile, not both. Please correct."); m->mothurOutEndLine(); abort = true; }
- if ((fastafile != "") && (namefile == "")) {
- vector<string> files; files.push_back(fastafile);
- parser.getNameFile(files);
- }
+ if (countfile == "") {
+ if ((fastafile != "") && (namefile == "")) {
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+ }
}
}
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
}
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
+ itTypes = outputTypes.find("taxonomy");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
if (namefile != "") { readNames(); } //fills names with all names in namefile.
else { getNames(); }//no name file, so get list of names to pick from
- GroupMap* groupMap;
+ GroupMap groupMap;
if (groupfile != "") {
-
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+ groupMap.readMap(groupfile);
//takes care of user setting groupNames that are invalid or setting groups=all
- SharedUtil* util = new SharedUtil();
- vector<string> namesGroups = groupMap->getNamesOfGroups();
- util->setGroups(Groups, namesGroups);
- delete util;
+ SharedUtil util;
+ vector<string> namesGroups = groupMap.getNamesOfGroups();
+ util.setGroups(Groups, namesGroups);
//file mismatch quit
- if (names.size() != groupMap->getNumSeqs()) {
- m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
+ if (names.size() != groupMap.getNumSeqs()) {
+ m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your groupfile contains " + toString(groupMap.getNumSeqs()) + ", please correct.");
m->mothurOutEndLine();
- delete groupMap;
return 0;
}
- }
+ }else if (countfile != "") {
+ if (ct.hasGroupInfo()) {
+ SharedUtil util;
+ vector<string> namesGroups = ct.getNamesOfGroups();
+ util.setGroups(Groups, namesGroups);
+ }
+
+ //file mismatch quit
+ if (names.size() != ct.getNumUniqueSeqs()) {
+ m->mothurOut("[ERROR]: your fasta file contains " + toString(names.size()) + " sequences, and your count file contains " + toString(ct.getNumUniqueSeqs()) + " unique sequences, please correct.");
+ m->mothurOutEndLine();
+ return 0;
+ }
+ }
if (m->control_pressed) { return 0; }
-
//make sure that if your picked groups size is not too big
- int thisSize = names.size();
+ int thisSize = 0;
+ if (countfile == "") { thisSize = names.size(); }
+ else { thisSize = ct. getNumSeqs(); } //all seqs not just unique
+
if (persample) {
if (size == 0) { //user has not set size, set size = smallest samples size
- size = groupMap->getNumSeqs(Groups[0]);
+ if (countfile == "") { size = groupMap.getNumSeqs(Groups[0]); }
+ else { size = ct.getGroupCount(Groups[0]); }
+
for (int i = 1; i < Groups.size(); i++) {
- int thisSize = groupMap->getNumSeqs(Groups[i]);
+ int thisSize = 0;
+ if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
+ else { thisSize = ct.getGroupCount(Groups[i]); }
if (thisSize < size) { size = thisSize; }
}
}else { //make sure size is not too large
vector<string> newGroups;
for (int i = 0; i < Groups.size(); i++) {
- int thisSize = groupMap->getNumSeqs(Groups[i]);
+ int thisSize = 0;
+ if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
+ else { thisSize = ct.getGroupCount(Groups[i]); }
if (thisSize >= size) { newGroups.push_back(Groups[i]); }
else { m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
}
Groups = newGroups;
+ if (newGroups.size() == 0) { m->mothurOut("[ERROR]: all groups removed."); m->mothurOutEndLine(); m->control_pressed = true; }
}
m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
if (pickedGroups) {
int total = 0;
for(int i = 0; i < Groups.size(); i++) {
- total += groupMap->getNumSeqs(Groups[i]);
+ if (countfile == "") { total += groupMap.getNumSeqs(Groups[i]); }
+ else { total += ct.getGroupCount(Groups[i]); }
}
if (size == 0) { //user has not set size, set size = 10% samples size
}
if (size == 0) { //user has not set size, set size = 10% samples size
- size = int (names.size() * 0.10);
+ if (countfile == "") { size = int (names.size() * 0.10); }
+ else { size = int (ct.getNumSeqs() * 0.10); }
}
- if (size > thisSize) { m->mothurOut("Your fasta file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
- size = thisSize;
- }
-
- if (!pickedGroups) { m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine(); }
+
+ if (size > thisSize) { m->mothurOut("Your fasta file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
+ size = thisSize;
+ }
+
+ if (!pickedGroups) { m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine(); }
}
random_shuffle(names.begin(), names.end());
set<string> subset; //dont want repeat sequence names added
if (persample) {
- //initialize counts
- map<string, int> groupCounts;
- map<string, int>::iterator itGroupCounts;
- for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
+ if (countfile == "") {
+ //initialize counts
+ map<string, int> groupCounts;
+ map<string, int>::iterator itGroupCounts;
+ for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
- for (int j = 0; j < names.size(); j++) {
+ for (int j = 0; j < names.size(); j++) {
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { return 0; }
- string group = groupMap->getGroup(names[j]);
- if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
- else{
- itGroupCounts = groupCounts.find(group);
- if (itGroupCounts != groupCounts.end()) {
- if (groupCounts[group] < size) { subset.insert(names[j]); groupCounts[group]++; }
- }
- }
- }
+ string group = groupMap.getGroup(names[j]);
+ if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
+ else{
+ itGroupCounts = groupCounts.find(group);
+ if (itGroupCounts != groupCounts.end()) {
+ if (itGroupCounts->second < size) { subset.insert(names[j]); (itGroupCounts->second)++; }
+ }
+ }
+ }
+ }else {
+ SubSample sample;
+ CountTable sampledCt = sample.getSample(ct, size, Groups);
+ vector<string> sampledSeqs = sampledCt.getNamesOfSeqs();
+ for (int i = 0; i < sampledSeqs.size(); i++) { subset.insert(sampledSeqs[i]); }
+
+ string countOutputDir = outputDir;
+ if (outputDir == "") { countOutputDir += m->hasPath(countfile); }
+ map<string, string> variables;
+ variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string countOutputFileName = getOutputFileName("count", variables);
+ outputTypes["count"].push_back(countOutputFileName); outputNames.push_back(countOutputFileName);
+ sampledCt.printTable(countOutputFileName);
+ }
}else {
-
- //randomly select a subset of those names to include in the subsample
- //since names was randomly shuffled just grab the next one
- for (int j = 0; j < names.size(); j++) {
-
- if (m->control_pressed) { return 0; }
-
- if (groupfile != "") { //if there is a groupfile given fill in group info
- string group = groupMap->getGroup(names[j]);
- if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
-
- if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
- if (m->inUsersGroups(group, Groups)) {
- subset.insert(names[j]);
- }
- }else{
- subset.insert(names[j]);
- }
- }else{ //save everyone, group
- subset.insert(names[j]);
- }
-
- //do we have enough??
- if (subset.size() == size) { break; }
- }
+ if (countfile == "") {
+ //randomly select a subset of those names to include in the subsample
+ //since names was randomly shuffled just grab the next one
+ for (int j = 0; j < names.size(); j++) {
+
+ if (m->control_pressed) { return 0; }
+
+ if (groupfile != "") { //if there is a groupfile given fill in group info
+ string group = groupMap.getGroup(names[j]);
+ if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
+
+ if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
+ if (m->inUsersGroups(group, Groups)) { subset.insert(names[j]); }
+ }else{ subset.insert(names[j]); }
+ }else{ //save everyone, group
+ subset.insert(names[j]);
+ }
+
+ //do we have enough??
+ if (subset.size() == size) { break; }
+ }
+ }else {
+ SubSample sample;
+ CountTable sampledCt = sample.getSample(ct, size, Groups, pickedGroups);
+ vector<string> sampledSeqs = sampledCt.getNamesOfSeqs();
+ for (int i = 0; i < sampledSeqs.size(); i++) { subset.insert(sampledSeqs[i]); }
+
+ string countOutputDir = outputDir;
+ if (outputDir == "") { countOutputDir += m->hasPath(countfile); }
+ map<string, string> variables;
+ variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string countOutputFileName = getOutputFileName("count", variables);
+ outputTypes["count"].push_back(countOutputFileName); outputNames.push_back(countOutputFileName);
+ sampledCt.printTable(countOutputFileName);
+ }
}
if (subset.size() == 0) { m->mothurOut("The size you selected is too large, skipping fasta file."); m->mothurOutEndLine(); return 0; }
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "subsample" + m->getExtension(fastafile);
-
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
}
in.close();
out.close();
+
if (count != subset.size()) {
m->mothurOut("[ERROR]: The subset selected contained " + toString(subset.size()) + " sequences, but I only found " + toString(count) + " of those in the fastafile."); m->mothurOutEndLine();
if (namefile != "") {
m->mothurOut("Deconvoluting subsampled fasta file... "); m->mothurOutEndLine();
-
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputNameFileName = getOutputFileName("name", variables);
//use unique.seqs to create new name and fastafile
string inputString = "fasta=" + outputFileName;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
delete uniqueCommand;
m->mothurCalling = false;
- outputTypes["name"].push_back(filenames["name"][0]); outputNames.push_back(filenames["name"][0]);
- m->mothurRemove(outputFileName);
- outputFileName = filenames["fasta"][0];
-
+ m->renameFile(filenames["name"][0], outputNameFileName);
+ m->renameFile(filenames["fasta"][0], outputFileName);
+
+ outputTypes["name"].push_back(outputNameFileName); outputNames.push_back(outputNameFileName);
+
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Done."); m->mothurOutEndLine();
- }
+
+ if (taxonomyfile != "") {
+ set<string> tempSubset;
+ //get new unique names from fasta file
+ //read through fasta file outputting only the names on the subsample list after deconvolute
+ ifstream in2;
+ m->openInputFile(outputFileName, in2);
+
+ while (!in2.eof()) {
+ Sequence seq(in2); m->gobble(in2);
+ if (seq.getName() != "") {
+ tempSubset.insert(seq.getName());
+ }
+ }
+ in2.close();
+
+ //send that list to getTax
+ int tcount = getTax(tempSubset);
+ if (tcount != tempSubset.size()) { m->mothurOut("[ERROR]: subsampled fasta file contains " + toString(tempSubset.size()) + " sequences, but I only found " + toString(tcount) + " in your taxonomy file, please correct."); m->mothurOutEndLine(); }
+ }
+ }else {
+ if (taxonomyfile != "") {
+ int tcount = getTax(subset);
+ if (tcount != subset.size()) { m->mothurOut("[ERROR]: subsampled fasta file contains " + toString(subset.size()) + " sequences, but I only found " + toString(tcount) + " in your taxonomy file, please correct."); m->mothurOutEndLine(); }
+
+ } //should only contain uniques.
+ }
outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
string groupOutputDir = outputDir;
if (outputDir == "") { groupOutputDir += m->hasPath(groupfile); }
- string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = groupOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string groupOutputFileName = getOutputFileName("group", variables);
ofstream outGroup;
m->openOutputFile(groupOutputFileName, outGroup);
int SubSampleCommand::readNames() {
try {
- ifstream in;
- m->openInputFile(namefile, in);
-
- string thisname, repnames;
- map<string, vector<string> >::iterator it;
-
- while(!in.eof()){
-
- if (m->control_pressed) { in.close(); return 0; }
-
- in >> thisname; m->gobble(in); //read from first column
- in >> repnames; //read from second column
-
- it = nameMap.find(thisname);
- if (it == nameMap.end()) {
-
- vector<string> splitRepNames;
- m->splitAtComma(repnames, splitRepNames);
-
- nameMap[thisname] = splitRepNames;
- for (int i = 0; i < splitRepNames.size(); i++) { names.push_back(splitRepNames[i]); }
-
- }else{ m->mothurOut(thisname + " is already in namesfile. I will use first definition."); m->mothurOutEndLine(); }
-
- m->gobble(in);
- }
- in.close();
-
+ nameMap.clear();
+ m->readNames(namefile, nameMap);
+
+ //save names of all sequences
+ map<string, vector<string> >::iterator it;
+ for (it = nameMap.begin(); it != nameMap.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { names.push_back((it->second)[i]); } }
+
return 0;
}
try {
//save mothurOut's binLabels to restore for next label
- vector<string> saveBinLabels = m->currentBinLabels;
+ vector<string> saveBinLabels = m->currentSharedBinLabels;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + ".subsample" + m->getExtension(sharedfile);
-
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[extension]"] = m->getExtension(sharedfile);
+ variables["[distance]"] = thislookup[0]->getLabel();
+ string outputFileName = getOutputFileName("shared", variables);
SubSample sample;
vector<string> subsampledLabels = sample.getSample(thislookup, size);
m->openOutputFile(outputFileName, out);
outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
- m->currentBinLabels = subsampledLabels;
+ m->currentSharedBinLabels = subsampledLabels;
thislookup[0]->printHeaders(out);
//save mothurOut's binLabels to restore for next label
- m->currentBinLabels = saveBinLabels;
+ m->currentSharedBinLabels = saveBinLabels;
return 0;
//**********************************************************************************************************************
int SubSampleCommand::getSubSampleList() {
try {
-
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "subsample" + m->getExtension(listfile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
- outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
+
+ if (namefile != "") { m->readNames(namefile, nameMap); }
+
InputData* input = new InputData(listfile, "list");
ListVector* list = input->getListVector();
string lastLabel = list->getLabel();
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
-
+
ofstream outGroup;
- GroupMap* groupMap;
+ GroupMap groupMap;
if (groupfile != "") {
-
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+ groupMap.readMap(groupfile);
//takes care of user setting groupNames that are invalid or setting groups=all
- SharedUtil* util = new SharedUtil();
- vector<string> namesGroups = groupMap->getNamesOfGroups();
- util->setGroups(Groups, namesGroups);
- delete util;
+ SharedUtil util; vector<string> namesGroups = groupMap.getNamesOfGroups(); util.setGroups(Groups, namesGroups);
//create outputfiles
string groupOutputDir = outputDir;
if (outputDir == "") { groupOutputDir += m->hasPath(groupfile); }
string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "subsample" + m->getExtension(groupfile);
-
m->openOutputFile(groupOutputFileName, outGroup);
outputTypes["group"].push_back(groupOutputFileName); outputNames.push_back(groupOutputFileName);
//file mismatch quit
- if (list->getNumSeqs() != groupMap->getNumSeqs()) {
- m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
+ if (list->getNumSeqs() != groupMap.getNumSeqs()) {
+ m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your groupfile contains " + toString(groupMap.getNumSeqs()) + ", please correct.");
+ m->mothurOutEndLine(); delete list; delete input; outGroup.close(); return 0;
+ }
+ }else if (countfile != "") {
+ if (ct.hasGroupInfo()) {
+ SharedUtil util;
+ vector<string> namesGroups = ct.getNamesOfGroups();
+ util.setGroups(Groups, namesGroups);
+ }
+
+ //file mismatch quit
+ if (list->getNumSeqs() != ct.getNumUniqueSeqs()) {
+ m->mothurOut("[ERROR]: your list file contains " + toString(list->getNumSeqs()) + " sequences, and your count file contains " + toString(ct.getNumUniqueSeqs()) + " unique sequences, please correct.");
m->mothurOutEndLine();
- delete groupMap;
- delete list;
- delete input;
- out.close();
- outGroup.close();
return 0;
- }
- }
-
+ }
+ }
+
//make sure that if your picked groups size is not too big
if (persample) {
if (size == 0) { //user has not set size, set size = smallest samples size
- size = groupMap->getNumSeqs(Groups[0]);
+ if (countfile == "") { size = groupMap.getNumSeqs(Groups[0]); }
+ else { size = ct.getGroupCount(Groups[0]); }
+
for (int i = 1; i < Groups.size(); i++) {
- int thisSize = groupMap->getNumSeqs(Groups[i]);
+ int thisSize = 0;
+ if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
+ else { thisSize = ct.getGroupCount(Groups[i]); }
if (thisSize < size) { size = thisSize; }
}
}else { //make sure size is not too large
vector<string> newGroups;
for (int i = 0; i < Groups.size(); i++) {
- int thisSize = groupMap->getNumSeqs(Groups[i]);
+ int thisSize = 0;
+ if (countfile == "") { thisSize = groupMap.getNumSeqs(Groups[i]); }
+ else { thisSize = ct.getGroupCount(Groups[i]); }
if (thisSize >= size) { newGroups.push_back(Groups[i]); }
else { m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
}
Groups = newGroups;
+ if (newGroups.size() == 0) { m->mothurOut("[ERROR]: all groups removed."); m->mothurOutEndLine(); m->control_pressed = true; }
}
- m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
+ m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
}else{
- if (pickedGroups) {
+ if (pickedGroups) {
int total = 0;
for(int i = 0; i < Groups.size(); i++) {
- total += groupMap->getNumSeqs(Groups[i]);
+ if (countfile == "") { total += groupMap.getNumSeqs(Groups[i]); }
+ else { total += ct.getGroupCount(Groups[i]); }
}
if (size == 0) { //user has not set size, set size = 10% samples size
}
if (total < size) {
- m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
+ if (size != 0) {
+ m->mothurOut("Your size is too large for the number of groups you selected. Adjusting to " + toString(int (total * 0.10)) + "."); m->mothurOutEndLine();
+ }
size = int (total * 0.10);
}
m->mothurOut("Sampling " + toString(size) + " from " + toString(total) + "."); m->mothurOutEndLine();
- }else{
-
- if (size == 0) { //user has not set size, set size = 10% samples size
- size = int (list->getNumSeqs() * 0.10);
+ }else {
+ if (size == 0) { //user has not set size, set size = 10% samples size
+ if (countfile == "") { size = int (list->getNumSeqs() * 0.10); }
+ else { size = int (ct.getNumSeqs() * 0.10); }
}
- int thisSize = list->getNumSeqs();
+ int thisSize = 0;
+ if (countfile == "") { thisSize = list->getNumSeqs(); }
+ else { thisSize = ct.getNumSeqs(); }
+
if (size > thisSize) { m->mothurOut("Your list file only contains " + toString(thisSize) + " sequences. Setting size to " + toString(thisSize) + "."); m->mothurOutEndLine();
size = thisSize;
}
- m->mothurOut("Sampling " + toString(size) + " from " + toString(list->getNumSeqs()) + "."); m->mothurOutEndLine();
- }
- }
-
-
- //fill names
- for (int i = 0; i < list->getNumBins(); i++) {
- string binnames = list->get(i);
-
- //parse names
- string individual = "";
- int length = binnames.length();
- for(int j=0;j<length;j++){
- if(binnames[j] == ','){
-
- if (groupfile != "") { //if there is a groupfile given fill in group info
- string group = groupMap->getGroup(individual);
- if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
-
- if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
- if (m->inUsersGroups(group, Groups)) {
- names.push_back(individual);
- }
- }else{
- names.push_back(individual);
- }
- }else{ //save everyone, group
- names.push_back(individual);
- }
- individual = "";
- }
- else{
- individual += binnames[j];
- }
- }
- //save last name
- if (groupfile != "") { //if there is a groupfile given fill in group info
- string group = groupMap->getGroup(individual);
- if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
-
- if (pickedGroups) { //if hte user picked groups, we only want to keep the names of sequences from those groups
- if (m->inUsersGroups(group, Groups)) {
- names.push_back(individual);
- }
- }else{
- names.push_back(individual);
- }
- }else{ //save everyone, group
- names.push_back(individual);
- }
- }
-
- random_shuffle(names.begin(), names.end());
-
- //randomly select a subset of those names to include in the subsample
- set<string> subset; //dont want repeat sequence names added
- if (persample) {
- //initialize counts
- map<string, int> groupCounts;
- map<string, int>::iterator itGroupCounts;
- for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
-
- for (int j = 0; j < names.size(); j++) {
-
- if (m->control_pressed) { return 0; }
-
- string group = groupMap->getGroup(names[j]);
- if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
- else{
- itGroupCounts = groupCounts.find(group);
- if (itGroupCounts != groupCounts.end()) {
- if (groupCounts[group] < size) { subset.insert(names[j]); groupCounts[group]++; }
- }
- }
- }
- }else{
- for (int j = 0; j < size; j++) {
-
- if (m->control_pressed) { break; }
-
- subset.insert(names[j]);
- }
- }
-
- if (groupfile != "") {
- //write out new groupfile
- for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
- string group = groupMap->getGroup(*it);
- if (group == "not found") { group = "NOTFOUND"; }
-
- outGroup << *it << '\t' << group << endl;
- }
- outGroup.close(); delete groupMap;
- }
-
+ m->mothurOut("Sampling " + toString(size) + " from " + toString(thisSize) + "."); m->mothurOutEndLine();
+ }
+ }
+
+ set<string> subset; //dont want repeat sequence names added
+ if (countfile == "") {
+ //fill names
+ for (int i = 0; i < list->getNumBins(); i++) {
+ string binnames = list->get(i);
+ vector<string> thisBin;
+ m->splitAtComma(binnames, thisBin);
+
+ for(int j=0;j<thisBin.size();j++){
+ if (groupfile != "") { //if there is a groupfile given fill in group info
+ string group = groupMap.getGroup(thisBin[j]);
+ if (group == "not found") { m->mothurOut("[ERROR]: " + thisBin[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
+
+ //if hte user picked groups, we only want to keep the names of sequences from those groups
+ if (pickedGroups) { if (m->inUsersGroups(group, Groups)) { names.push_back(thisBin[j]); } }
+ else{ names.push_back(thisBin[j]); }
+ }//save everyone, group
+ else{ names.push_back(thisBin[j]); }
+ }
+ }
+
+ random_shuffle(names.begin(), names.end());
+
+ //randomly select a subset of those names to include in the subsample
+ if (persample) {
+ //initialize counts
+ map<string, int> groupCounts;
+ map<string, int>::iterator itGroupCounts;
+ for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
+
+ for (int j = 0; j < names.size(); j++) {
+
+ if (m->control_pressed) { delete list; delete input; return 0; }
+
+ string group = groupMap.getGroup(names[j]);
+ if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
+ else{
+ itGroupCounts = groupCounts.find(group);
+ if (itGroupCounts != groupCounts.end()) {
+ if (groupCounts[group] < size) { subset.insert(names[j]); groupCounts[group]++; }
+ }
+ }
+ }
+ }else{
+ for (int j = 0; j < size; j++) {
+ if (m->control_pressed) { break; }
+ subset.insert(names[j]);
+ }
+ }
+
+ if (groupfile != "") {
+ //write out new groupfile
+ for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) {
+ string group = groupMap.getGroup(*it);
+ if (group == "not found") { group = "NOTFOUND"; }
+ outGroup << *it << '\t' << group << endl;
+ }
+ outGroup.close();
+ }
+ }else {
+ SubSample sample; CountTable sampledCt;
+
+ if (persample) { sampledCt = sample.getSample(ct, size, Groups); }
+ else { sampledCt = sample.getSample(ct, size, Groups, pickedGroups); }
+
+ vector<string> sampledSeqs = sampledCt.getNamesOfSeqs();
+ for (int i = 0; i < sampledSeqs.size(); i++) { subset.insert(sampledSeqs[i]); }
+
+ string countOutputDir = outputDir;
+ if (outputDir == "") { countOutputDir += m->hasPath(countfile); }
+ map<string, string> variables;
+ variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string countOutputFileName = getOutputFileName("count", variables);
+ outputTypes["count"].push_back(countOutputFileName); outputNames.push_back(countOutputFileName);
+ sampledCt.printTable(countOutputFileName);
+ }
//as long as you are not at the end of the file or done wih the lines you want
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { delete list; delete input; out.close(); return 0; }
+ if (m->control_pressed) { delete list; delete input; return 0; }
if(allLines == 1 || labels.count(list->getLabel()) == 1){
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
- processList(list, out, subset);
+ processList(list, subset);
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
list = input->getListVector(lastLabel);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
- processList(list, out, subset);
+ processList(list, subset);
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
}
- if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); return 0; }
+ if (m->control_pressed) { if (list != NULL) { delete list; } delete input; return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
- processList(list, out, subset);
+ processList(list, subset);
delete list; list = NULL;
}
- out.close();
if (list != NULL) { delete list; }
delete input;
+
+ if (taxonomyfile != "") {
+ if (namefile == "") {
+ InputData input(listfile, "list");
+ ListVector* list = input.getListVector();
+ string lastLabel = list->getLabel();
+
+ for (int i = 0; i < list->getNumBins(); i++) {
+ vector<string> temp;
+ string bin = list->get(i);
+ m->splitAtComma(bin, temp);
+ for (int j = 0; j < temp.size(); j++) { vector<string> tempFakeOut; tempFakeOut.push_back(temp[j]); nameMap[temp[j]] = tempFakeOut; }
+ }
+ delete list;
+
+ int tcount = getTax(subset);
+ if (tcount != subset.size()) { m->mothurOut("[ERROR]: subsampled list file contains " + toString(subset.size()) + " sequences, but I only found " + toString(tcount) + " in your taxonomy file, did you forget a name file? Please correct."); m->mothurOutEndLine(); }
+ }else {
+ string tempAccnos = "temp.accnos";
+ ofstream outAccnos;
+ m->openOutputFile(tempAccnos, outAccnos);
+ for (set<string>::iterator it = subset.begin(); it != subset.end(); it++) { outAccnos << *it << endl; }
+ outAccnos.close();
+
+ m->mothurOut("Sampling taxonomy and name file... "); m->mothurOutEndLine();
+ string thisNameOutputDir = outputDir;
+ if (outputDir == "") { thisNameOutputDir += m->hasPath(namefile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisNameOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputNameFileName = getOutputFileName("name", variables);
+
+ string thisTaxOutputDir = outputDir;
+ if (outputDir == "") { thisTaxOutputDir += m->hasPath(taxonomyfile); }
+ variables["[filename]"] = thisTaxOutputDir + m->getRootName(m->getSimpleName(taxonomyfile));
+ variables["[extension]"] = m->getExtension(taxonomyfile);
+ string outputTaxFileName = getOutputFileName("taxonomy", variables);
+
+
+ //use unique.seqs to create new name and fastafile
+ string inputString = "dups=f, name=" + namefile + ", taxonomy=" + taxonomyfile + ", accnos=" + tempAccnos;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: get.seqs(" + inputString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* getCommand = new GetSeqsCommand(inputString);
+ getCommand->execute();
+
+ map<string, vector<string> > filenames = getCommand->getOutputFiles();
+
+ delete getCommand;
+ m->mothurCalling = false;
+
+ m->renameFile(filenames["name"][0], outputNameFileName);
+ m->renameFile(filenames["taxonomy"][0], outputTaxFileName);
+
+ outputTypes["name"].push_back(outputNameFileName); outputNames.push_back(outputNameFileName);
+ outputNames.push_back(outputTaxFileName); outputTypes["taxonomy"].push_back(outputTaxFileName);
+
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ m->mothurOut("Done."); m->mothurOutEndLine();
+ }
+ }
return 0;
}
}
//**********************************************************************************************************************
-int SubSampleCommand::processList(ListVector*& list, ofstream& out, set<string>& subset) {
+int SubSampleCommand::processList(ListVector*& list, set<string>& subset) {
try {
-
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ variables["[distance]"] = list->getLabel();
+ string outputFileName = getOutputFileName("list", variables);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
int numBins = list->getNumBins();
ListVector* temp = new ListVector();
temp->setLabel(list->getLabel());
+ vector<string> binLabels = list->getLabels();
+ vector<string> newLabels;
for (int i = 0; i < numBins; i++) {
if (m->control_pressed) { break; }
- string binnames = list->get(i);
-
- //parse names
- string individual = "";
- string newNames = "";
- int length = binnames.length();
- for(int j=0;j<length;j++){
- if(binnames[j] == ','){
- if (subset.count(individual) != 0) { newNames += individual + ","; }
- individual = "";
- }else{
- individual += binnames[j];
- }
- }
- if (subset.count(individual) != 0) { newNames += individual + ","; }
+ string bin = list->get(i);
+ vector<string> binnames;
+ m->splitAtComma(bin, binnames);
+ string newNames = "";
+ for(int j=0;j<binnames.size();j++){ if (subset.count(binnames[j]) != 0) { newNames += binnames[j] + ","; } }
//if there are names in this bin add to new list
if (newNames != "") {
newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
temp->push_back(newNames);
+ newLabels.push_back(binLabels[i]);
}
}
+ temp->setLabels(newLabels);
delete list;
list = temp;
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { out.close(); return 0; }
+ list->printHeaders(out);
list->print(out);
+ out.close();
return 0;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "subsample" + m->getExtension(rabundfile);
-
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile));
+ variables["[extension]"] = m->getExtension(rabundfile);
+ string outputFileName = getOutputFileName("rabund", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "subsample" + m->getExtension(sabundfile);
-
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile));
+ variables["[extension]"] = m->getExtension(sabundfile);
+ string outputFileName = getOutputFileName("sabund", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->errorOut(e, "SubSampleCommand", "processSabund");
exit(1);
}
-}
+}
+
+//**********************************************************************************************************************
+int SubSampleCommand::getTax(set<string>& subset) {
+ try {
+
+ string thisTaxOutputDir = outputDir;
+ if (outputDir == "") { thisTaxOutputDir += m->hasPath(taxonomyfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisTaxOutputDir + m->getRootName(m->getSimpleName(taxonomyfile));
+ variables["[extension]"] = m->getExtension(taxonomyfile);
+ string outputTaxFileName = getOutputFileName("taxonomy", variables);
+ ofstream outTax;
+ m->openOutputFile(outputTaxFileName, outTax);
+ outputNames.push_back(outputTaxFileName); outputTypes["taxonomy"].push_back(outputTaxFileName);
+
+ //read through fasta file outputting only the names on the subsample list
+ ifstream inTax;
+ m->openInputFile(taxonomyfile, inTax);
+
+ string tname, tax;
+ int tcount = 0;
+ map<string, vector<string> >::iterator itNameMap;
+
+ while(!inTax.eof()){
+
+ if (m->control_pressed) { inTax.close(); outTax.close(); return 0; }
+
+ inTax >> tname; m->gobble(inTax); //read from first column
+ inTax >> tax; m->gobble(inTax); //read from second column
+
+ //does the subset contain a sequence that this sequence represents
+ itNameMap = nameMap.find(tname);
+ if (itNameMap != nameMap.end()) {
+ vector<string> nameRepresents = itNameMap->second;
+
+
+ for (int i = 0; i < nameRepresents.size(); i++){
+ if (subset.count(nameRepresents[i]) != 0) {
+ outTax << nameRepresents[i] << '\t' << tax << endl;
+ tcount++;
+
+ }
+ }
+ }else{ m->mothurOut("[ERROR]: " + tname + " is missing, please correct."); m->mothurOutEndLine(); }
+ }
+ inTax.close();
+ outTax.close();
+
+ return tcount;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSampleCommand", "getTax");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
projects / mothur.git / blobdiff