#include "subsamplecommand.h"
#include "sharedutilities.h"
+#include "deconvolutecommand.h"
//**********************************************************************************************************************
vector<string> SubSampleCommand::setParameters(){
set<string> subset; //dont want repeat sequence names added
if (persample) {
- for (int i = 0; i < Groups.size(); i++) {
-
- //randomly select a subset of those names from this group to include in the subsample
- for (int j = 0; j < size; j++) {
-
- if (m->control_pressed) { return 0; }
+ //initialize counts
+ map<string, int> groupCounts;
+ for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
+
+ for (int j = 0; j < names.size(); j++) {
- //get random sequence to add, making sure we have not already added it
- bool done = false;
- int myrand;
- while (!done) {
- myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0));
-
- if (subset.count(names[myrand]) == 0) {
-
- string group = groupMap->getGroup(names[myrand]);
- if (group == "not found") { m->mothurOut("[ERROR]: " + names[myrand] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
-
- if (group == Groups[i]) { subset.insert(names[myrand]); break; }
- }
- }
- }
+ 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{
+ if (groupCounts[group] < size) { subset.insert(names[j]); }
+ }
}
}else {
//randomly select a subset of those names to include in the subsample
- for (int j = 0; j < size; j++) {
+ //since names was randomly shuffled just grab the next one
+ for (int j = 0; j < names.size(); j++) {
if (m->control_pressed) { return 0; }
- //get random sequence to add, making sure we have not already added it
- bool done = false;
- int myrand;
- while (!done) {
- myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0));
+ 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 (subset.count(names[myrand]) == 0) {
-
- if (groupfile != "") { //if there is a groupfile given fill in group info
- string group = groupMap->getGroup(names[myrand]);
- if (group == "not found") { m->mothurOut("[ERROR]: " + names[myrand] + " 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[myrand]); break;
- }
- }else{
- subset.insert(names[myrand]); break;
- }
- }else{ //save everyone, group
- subset.insert(names[myrand]); break;
- }
+ 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; }
}
}
ofstream out;
m->openOutputFile(outputFileName, out);
- outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
//read through fasta file outputting only the names on the subsample list
ifstream in;
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();
+
+ //use unique.seqs to create new name and fastafile
+ string inputString = "fasta=" + outputFileName;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
+
+ Command* uniqueCommand = new DeconvoluteCommand(inputString);
+ uniqueCommand->execute();
+
+ map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
+
+ delete uniqueCommand;
+
+ outputTypes["name"].push_back(filenames["name"][0]); outputNames.push_back(filenames["name"][0]);
+ m->mothurRemove(outputFileName);
+ outputFileName = filenames["fasta"][0];
+
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ m->mothurOut("Done."); m->mothurOutEndLine();
+ }
+
+ outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
//if a groupfile is provided read through the group file only outputting the names on the subsample list
if (groupfile != "") {
if (m->control_pressed) { delete order; out.close(); return 0; }
//get random number to sample from order between 0 and thisSize-1.
- int myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0));
+ //don't need this because of the random shuffle above
+ //int myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0));
- int bin = order->get(myrand);
+ int bin = order->get(j);
int abund = thislookup[i]->getAbundance(bin);
thislookup[i]->set(bin, (abund+1), thisgroup);
//randomly select a subset of those names to include in the subsample
set<string> subset; //dont want repeat sequence names added
if (persample) {
- for (int i = 0; i < Groups.size(); i++) {
+ //initialize counts
+ map<string, int> groupCounts;
+ 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 < size; j++) {
-
- if (m->control_pressed) { break; }
-
- //get random sequence to add, making sure we have not already added it
- bool done = false;
- int myrand;
- while (!done) {
- myrand = int((float)(names.size()) * (float)(rand()) / ((float)RAND_MAX+1.0));
-
- if (subset.count(names[myrand]) == 0) { //you are not already added
- if (groupMap->getGroup(names[myrand]) == Groups[i]) { subset.insert(names[myrand]); break; }
- }
- }
- }
+ 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{
+ if (groupCounts[group] < size) { subset.insert(names[j]); }
+ }
}
}else{
for (int j = 0; j < size; j++) {
if (m->control_pressed) { break; }
- //get random sequence to add, making sure we have not already added it
- bool done = false;
- int myrand;
- while (!done) {
- myrand = int((float)(names.size()) * (float)(rand()) / ((float)RAND_MAX+1.0));
-
- if (subset.count(names[myrand]) == 0) { subset.insert(names[myrand]); break; }
- }
+ subset.insert(names[j]);
}
}
if (m->control_pressed) { delete order; return 0; }
- //get random number to sample from order between 0 and thisSize-1.
- int myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0));
-
- int bin = order->get(myrand);
+ int bin = order->get(j);
int abund = rabund->get(bin);
rabund->set(bin, (abund+1));
if (m->control_pressed) { delete order; return 0; }
- //get random number to sample from order between 0 and thisSize-1.
- int myrand = int((float)(thisSize) * (float)(rand()) / ((float)RAND_MAX+1.0));
-
- int bin = order->get(myrand);
+ int bin = order->get(j);
int abund = rabund->get(bin);
rabund->set(bin, (abund+1));
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