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//
// testoptirefmatrix.cpp
// Mothur
//
// Created by Sarah Westcott on 7/24/18.
// Copyright © 2018 Schloss Lab. All rights reserved.
//
#include "testoptirefmatrix.hpp"
#include "dataset.h"
/**************************************************************************************************/
TestOptiRefMatrix::TestOptiRefMatrix() { //setup
m = MothurOut::getInstance();
TestDataSet data;
filenames = data.getSubsetFNGFiles(); //Fasta, name, group returned
columnFile = data.getSubsetFNGDistFile();
phylipFile = data.getSubsetFNGPhylipDistFile();
reffilenames = data.getOptiRefFiles(); //fasta, count, column, phylip, list, betweendist returned
}
/**************************************************************************************************/
TestOptiRefMatrix::~TestOptiRefMatrix() {}
/**************************************************************************************************/
//distfile, distFormat, dupsFile, dupsFormat, cutoff, percentage to be fitseqs - will randomly assign as fit
TEST(Test_Container_OptiRefMatrix, readColumnDenovo) {
MothurOut* m; m = MothurOut::getInstance();
m->setRandomSeed(123456); //stabilize radomization
TestOptiRefMatrix testOMatrix;
OptiRefMatrix matrix(testOMatrix.columnFile, "column", testOMatrix.filenames[1], "name", 0.03, 50, "none");
//EXPECT_EQ(160,(matrix.print(cout)));
EXPECT_EQ(80,(matrix.getNumDists()));
EXPECT_EQ(17,(matrix.getNumFitDists()));
EXPECT_EQ(27,(matrix.getNumRefDists()));
vector<long long> refSeqs = matrix.getRefSeqs();
string Expected_ReturnResults = "1357111516181920222527283132333435373840414445474851535556";
string ReturnResults = "";
for (long long i = 0; i < refSeqs.size(); i++) { ReturnResults += toString(refSeqs[i]); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
long long sanityCheck = matrix.getNumDists() - (matrix.getNumFitDists() + matrix.getNumRefDists());
EXPECT_EQ(36,sanityCheck); //number of inbetween dists
}
//distfile, distFormat, dupsFile, dupsFormat, cutoff, percentage to be fitseqs - will randomly assign as fit
TEST(Test_Container_OptiRefMatrix, readPhylipDenovo) {
MothurOut* m; m = MothurOut::getInstance();
m->setRandomSeed(123456); //stabilize radomization
TestOptiRefMatrix testOMatrix;
OptiRefMatrix matrix(testOMatrix.phylipFile, "phylip", testOMatrix.filenames[1], "name", 0.03, 50, "none");
//EXPECT_EQ(160,(matrix.print(cout)));
EXPECT_EQ(80,(matrix.getNumDists()));
EXPECT_EQ(17,(matrix.getNumFitDists()));
EXPECT_EQ(22,(matrix.getNumRefDists()));
vector<long long> refSeqs = matrix.getRefSeqs();
string Expected_ReturnResults = "136791014161819212224282930323335363839414344455152535556";
string ReturnResults = "";
for (long long i = 0; i < refSeqs.size(); i++) { ReturnResults += toString(refSeqs[i]); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
long long sanityCheck = matrix.getNumDists() - (matrix.getNumFitDists() + matrix.getNumRefDists());
EXPECT_EQ(41,sanityCheck); //number of inbetween dists
}
//refdistfile, refname or refcount, refformat, refdistformat, cutoff, fitdistfile, fitname or fitcount, fitformat, fitdistformat, betweendistfile, betweendistformat - files for reference
TEST(Test_Container_OptiRefMatrix, readColumnReference) {
TestOptiRefMatrix testOMatrix;
OptiRefMatrix matrix(testOMatrix.reffilenames[2], testOMatrix.reffilenames[1], "count", "column", 0.03, testOMatrix.columnFile, testOMatrix.filenames[1], "name", "column", testOMatrix.reffilenames[5], "column");
//EXPECT_EQ(113772,(matrix.print(cout)));
EXPECT_EQ(56886,(matrix.getNumDists())); //unique dists 56886*2=113772
EXPECT_EQ(80,(matrix.getNumFitDists()));
EXPECT_EQ(56675,(matrix.getNumRefDists()));
long long sanityCheck = matrix.getNumDists() - (matrix.getNumFitDists() + matrix.getNumRefDists());
EXPECT_EQ(131,sanityCheck); //number of inbetween dists
}
//refdistfile, refname or refcount, refformat, refdistformat, cutoff, fitdistfile, fitname or fitcount, fitformat, fitdistformat, betweendistfile, betweendistformat - files for reference
TEST(Test_Container_OptiRefMatrix, readPhylipReference) {
TestOptiRefMatrix testOMatrix;
OptiRefMatrix matrix(testOMatrix.reffilenames[3], testOMatrix.reffilenames[1], "count", "phylip", 0.03, testOMatrix.columnFile, testOMatrix.filenames[1], "name", "column", testOMatrix.reffilenames[5], "column");
//EXPECT_EQ(113772,(matrix.print(cout)));
EXPECT_EQ(56893,(matrix.getNumDists())); //unique dists 56886*2=113772
EXPECT_EQ(80,(matrix.getNumFitDists()));
EXPECT_EQ(56682,(matrix.getNumRefDists()));
long long sanityCheck = matrix.getNumDists() - (matrix.getNumFitDists() + matrix.getNumRefDists());
EXPECT_EQ(131,sanityCheck); //number of inbetween dists
}
TEST(Test_Container_OptiRefMatrix, getNumCLose) {
MothurOut* m; m = MothurOut::getInstance();
m->setRandomSeed(123456); //stabilize radomization
TestOptiRefMatrix testOMatrix;
OptiRefMatrix matrix(testOMatrix.columnFile, "column", testOMatrix.filenames[1], "name", 0.03, 50, "none");
EXPECT_EQ(1,(matrix.getNumClose(0)));
EXPECT_EQ(2,(matrix.getNumClose(5)));
EXPECT_EQ(3,(matrix.getNumClose(10)));
EXPECT_EQ(7,(matrix.getNumClose(15)));
EXPECT_EQ(2,(matrix.getNumClose(20)));
EXPECT_EQ(1,(matrix.getNumFitClose(0)));
EXPECT_EQ(0,(matrix.getNumFitClose(5)));
EXPECT_EQ(1,(matrix.getNumFitClose(10)));
EXPECT_EQ(4,(matrix.getNumFitClose(15)));
EXPECT_EQ(0,(matrix.getNumFitClose(20)));
EXPECT_EQ(0,(matrix.getNumRefClose(0)));
EXPECT_EQ(2,(matrix.getNumRefClose(5)));
EXPECT_EQ(2,(matrix.getNumRefClose(10)));
EXPECT_EQ(3,(matrix.getNumRefClose(15)));
EXPECT_EQ(2,(matrix.getNumRefClose(20)));
}
TEST(Test_Container_OptiRefMatrix, isCloseFit) {
MothurOut* m; m = MothurOut::getInstance();
m->setRandomSeed(123456); //stabilize radomization
TestOptiRefMatrix testOMatrix;
OptiRefMatrix matrix(testOMatrix.columnFile, "column", testOMatrix.filenames[1], "name", 0.03, 50, "none");
bool isFit;
vector<long long> fitSeqs = matrix.getFitSeqs();
string Expected_ReturnResults = "024689101213141721232426293036394243464950525457";
string ReturnResults = "";
for (long long i = 0; i < fitSeqs.size(); i++) { ReturnResults += toString(fitSeqs[i]); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
//check closeness
EXPECT_EQ(true,(matrix.isClose(0, 8)));
EXPECT_EQ(true,(matrix.isClose(1, 28)));
EXPECT_EQ(true,(matrix.isClose(2, 44)));
EXPECT_EQ(true,(matrix.isClose(15, 42)));
EXPECT_EQ(true,(matrix.isClose(35, 36)));
//check not close
EXPECT_EQ(false,(matrix.isClose(57, 8)));
EXPECT_EQ(false,(matrix.isClose(47, 28)));
EXPECT_EQ(false,(matrix.isClose(32, 44)));
EXPECT_EQ(false,(matrix.isClose(23, 42)));
EXPECT_EQ(false,(matrix.isClose(12, 36)));
//assumes first value is a fitSeq
EXPECT_EQ(true,(matrix.isCloseFit(0, 8, isFit))); //both fit and close
EXPECT_EQ(true, isFit);
EXPECT_EQ(false,(matrix.isCloseFit(2, 28, isFit))); //not fit
EXPECT_EQ(false, isFit);
EXPECT_EQ(false,(matrix.isCloseFit(3, 20, isFit))); //not fit, but close
EXPECT_EQ(false, isFit);
EXPECT_EQ(false,(matrix.isCloseFit(13, 42, isFit))); //both fit, not close
EXPECT_EQ(true, isFit);
EXPECT_EQ(false,(matrix.isCloseFit(30, 36, isFit))); //both fit, not close
EXPECT_EQ(true, isFit);
}
TEST(Test_Container_OptiRefMatrix, getCloseFitSeqs) {
MothurOut* m; m = MothurOut::getInstance();
m->setRandomSeed(123456); //stabilize radomization
TestOptiRefMatrix testOMatrix;
OptiRefMatrix matrix(testOMatrix.columnFile, "column", testOMatrix.filenames[1], "name", 0.03, 50, "none");
//"024689101213141721232426293036394243464950525457";
//17 GQY1XT001BJ4H6,..,GQY1XT001CW8RQ 11 32 52 55 57
string Expected_ReturnResults = ""; Expected_ReturnResults += "52"; Expected_ReturnResults += "57";
set<long long> temp = matrix.getCloseFitSeqs(17);
string ReturnResults = "";
for (set<long long>::iterator it = temp.begin(); it != temp.end(); it++) { ReturnResults += toString(*it); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
//50 GQY1XT001EK1FO 13
Expected_ReturnResults = ""; Expected_ReturnResults += "13";
temp = matrix.getCloseFitSeqs(50);
ReturnResults = "";
for (set<long long>::iterator it = temp.begin(); it != temp.end(); it++) { ReturnResults += toString(*it); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
//52 GQY1XT001ENMKV 11 17 32 55 57
Expected_ReturnResults = ""; Expected_ReturnResults += "17"; Expected_ReturnResults += "57";
temp = matrix.getCloseFitSeqs(52);
ReturnResults = "";
for (set<long long>::iterator it = temp.begin(); it != temp.end(); it++) { ReturnResults += toString(*it); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
//36 GQY1XT001DHDV0,GQY1XT001B0UFF 15 24 35 38
Expected_ReturnResults = ""; Expected_ReturnResults += "24";
temp = matrix.getCloseFitSeqs(36);
ReturnResults = "";
for (set<long long>::iterator it = temp.begin(); it != temp.end(); it++) { ReturnResults += toString(*it); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
//21 GQY1XT001BUMO0 26 42 46
Expected_ReturnResults = ""; Expected_ReturnResults += "26"; Expected_ReturnResults += "42"; Expected_ReturnResults += "46";
temp = matrix.getCloseFitSeqs(21);
ReturnResults = "";
for (set<long long>::iterator it = temp.begin(); it != temp.end(); it++) { ReturnResults += toString(*it); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
}
TEST(Test_Container_OptiRefMatrix, extractRefMatrix) {
MothurOut* m; m = MothurOut::getInstance();
m->setRandomSeed(123456); //stabilize radomization
TestOptiRefMatrix testOMatrix;
OptiRefMatrix matrix(testOMatrix.columnFile, "column", testOMatrix.filenames[1], "name", 0.03, 50, "none");
OptiData* refMatrix = matrix.extractRefMatrix();
//EXPECT_EQ(54,(refMatrix->print(cout)));
EXPECT_EQ(54,(refMatrix->getNumDists()));
}
TEST(Test_Container_OptiRefMatrix, extractMatrixSubset) {
MothurOut* m; m = MothurOut::getInstance();
m->setRandomSeed(123456); //stabilize radomization
TestOptiRefMatrix testOMatrix;
OptiRefMatrix matrix(testOMatrix.columnFile, "column", testOMatrix.filenames[1], "name", 0.03, 50, "none");
vector<long long> temp = matrix.getFitSeqs();
set<long long> fitSeqs;
for (long long i = 0; i < temp.size(); i++) { fitSeqs.insert(temp[i]); }
OptiData* fitMatrix = matrix.extractMatrixSubset(fitSeqs);
//EXPECT_EQ(34,(fitMatrix->print(cout)));
EXPECT_EQ(34,(fitMatrix->getNumDists()));
}
TEST(Test_Container_OptiRefMatrix, getFitListSingle) {
MothurOut* m; m = MothurOut::getInstance();
m->setRandomSeed(123456); //stabilize radomization
TestOptiRefMatrix testOMatrix;
OptiRefMatrix matrix(testOMatrix.columnFile, "column", testOMatrix.filenames[1], "name", 0.03, 50, "none");
//maps names to index in closeness matrix
ListVector* fitListSingle = matrix.getFitListSingle();
//check bin 0
string bin = fitListSingle->get(0);
EXPECT_EQ("GQY1XT001AD34Z", bin);
bin = fitListSingle->get(10);
EXPECT_EQ("GQY1XT001CH9UX,GQY1XT001C80OT,GQY1XT001BEIF2,GQY1XT001DFU9M,GQY1XT001DNJRS", bin);
bin = fitListSingle->get(16);
EXPECT_EQ("GQY1XT001EACH9", bin);
bin = fitListSingle->get(3);
EXPECT_EQ("GQY1XT001B8C4W,GQY1XT001DBTGA,GQY1XT001B4VQ6", bin);
bin = fitListSingle->get(7);
EXPECT_EQ("GQY1XT001C4UVG", bin);
}
TEST(Test_Container_OptiRefMatrix, randomizeRefs) {
MothurOut* m; m = MothurOut::getInstance();
m->setRandomSeed(123456); //stabilize radomization
TestOptiRefMatrix testOMatrix;
OptiRefMatrix matrix(testOMatrix.columnFile, "column", testOMatrix.filenames[1], "name", 0.03, 50, "none");
matrix.randomizeRefs();
vector<long long> refSeqs = matrix.getRefSeqs();
string Expected_ReturnResults = "0135678112023242629313236394041434547525356";
string ReturnResults = "";
for (long long i = 0; i < refSeqs.size(); i++) { ReturnResults += toString(refSeqs[i]); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
matrix.randomizeRefs();
refSeqs = matrix.getRefSeqs();
Expected_ReturnResults = "3467891315161718202122232426273132333536373841474950";
ReturnResults = "";
for (long long i = 0; i < refSeqs.size(); i++) { ReturnResults += toString(refSeqs[i]); }
EXPECT_EQ(Expected_ReturnResults, ReturnResults);
}
/**************************************************************************************************/
|
