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//
// testvsearchfileparser.cpp
// Mothur
//
// Created by Sarah Westcott on 3/24/16.
// Copyright (c) 2016 Schloss Lab. All rights reserved.
//
#include "testvsearchfileparser.h"
/**************************************************************************************************/
TestVsearchFileParser::TestVsearchFileParser() { //setup
m = MothurOut::getInstance();
TestDataSet data;
filenames = data.getSubsetFNGFiles();
ct = data.getCountTable();
}
/**************************************************************************************************/
TestVsearchFileParser::~TestVsearchFileParser() {
delete ct;
}
/**************************************************************************************************
TEST_CASE("Testing VsearchParser Class") {
TestVsearchFileParser testVParser;
VsearchFileParser vsearchParser(testVParser.filenames[0], testVParser.filenames[1], "name");
SECTION("CreateVsearchFasta") {
INFO("Using First 100 sequences of final.fasta and final.names") // Only appears on a FAIL
CAPTURE(vsearchParser.getVsearchFile()); // Displays this variable on a FAIL
CHECK(vsearchParser.getVsearchFile() == "tempSeqs.txt.sorted.fasta.temp");
ifstream in;
testVParser.util.openInputFile(vsearchParser.getVsearchFile(), in);
while (!in.eof()) {
Sequence seq(in); testVParser.util.gobble(in);
vector<string> pieces;
string name = seq.getName();
testVParser.util.splitAtChar(name, pieces, '=');
string abundString = pieces[1].substr(0, pieces[1].length()-1);
int abund = 0;
testVParser.util.mothurConvert(abundString, abund);
int totalSeqs = testVParser.ct->getNumSeqs(testVParser.removeAbundances(name));
CHECK(abund == totalSeqs);
}
in.close();
testVParser.util.mothurRemove("tempSeqs.txt.sorted.fasta.temp");
}
SECTION("Remove Abundances") {
INFO("Using GQY1XT001C44N8/size=3677/") // Only appears on a FAIL
string seqName = "GQY1XT001C44N8/size=3677/";
CAPTURE(testVParser.removeAbundances(seqName)); // Displays this variable on a FAIL
CHECK(testVParser.removeAbundances(seqName) == "GQY1XT001C44N8");
}
SECTION("Create List File") {
INFO("Using lines like: S 1 275 * * * * * GQY1XT001C44N8/ab=3677/ *") // Only appears on a FAIL
vsearchParser.getVsearchFile();
ifstream in;
testVParser.util.openInputFile(vsearchParser.getVsearchFile(), in);
vector<string> seqNames;
while (!in.eof()) {
Sequence seq(in); testVParser.util.gobble(in);
string name = seq.getName();
seqNames.push_back(name);
}
in.close();
testVParser.util.mothurRemove("tempSeqs.txt.sorted.fasta.temp");
ofstream out;
testVParser.util.openOutputFile("temp.txt", out);
map<int, string> binNames;
for (int i = 0; i < seqNames.size(); i++) {
int bin = (i+1)%10;
string name = testVParser.removeAbundances(seqNames[i]);
//name = (testVParser.data.getNameMap())[name]; //dup names
out << "S\t" + toString(bin) + "\t275\t*\t*\t*\t*\t*\t" + seqNames[i] + "\t*\n";
map<int, string>::iterator it = binNames.find(bin);
if (it != binNames.end()) { it->second += "," + name; }
else { binNames[bin] = name; }
}
out.close();
int numBins = binNames.size();
testVParser.createListFile("temp.txt", "temp.list", "temp.rabund", "temp.sabund", numBins, "0.03");
ifstream in2;
testVParser.util.openInputFile("temp.list", in2);
ListVector list2(in2);
in2.close();
testVParser.util.mothurRemove("temp.list"); testVParser.util.mothurRemove("temp.rabund"); testVParser.util.mothurRemove("temp.sabund");
//for each bin
for (int i = 0; i < list2.getNumBins(); i++) {
string binnames = list2.get(i);
CAPTURE(binnames);
CHECK(binnames == binNames[i]);
}
}
}*/
/**************************************************************************************************/
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