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main.cpp
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main.cpp
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//
// main.cpp
// APOBECXP
//
// Created by Marat Kazanov on 07/03/2018.
// Copyright © 2018 Marat Kazanov. All rights reserved.
//
#include "apobec.hpp"
#include "allmotifs.hpp"
#include "options.h"
#include <fstream>
#include <iostream>
#include <set>
#include "mutation.hpp"
#include "signanalysis.hpp"
#include "CASEclusters.hpp"
int main(int argc, const char * argv[]) {
//ProcessClusters();
MakeApobecMutationsFile();
return 0;
vector<string> cancers;
vector<string> samples;
CHumanGenome human;
human.InitializeHuman("37", HUMAN_PATH, ".fa", "FASTA");
CMutations m;
cancers.push_back("CESC");
m.LoadMutations(CANCER_MUTATIONS_FILEFORMAT, CANCER_MUTATIONS_PATH, cancers, samples, 1, &human);
m.RenameSamples("/Users/mar/BIO/PROJECTS/PCAWG_APOBEC/PCAWG_samples_list.csv",2,3,16);
CSignatureAnalysis a;
a.signatures.push_back(CMutationSignature("TCA",2,"T"));
a.signatures.push_back(CMutationSignature("TCT",2,"T"));
a.signatures.push_back(CMutationSignature("TCA",2,"G"));
a.signatures.push_back(CMutationSignature("TCT",2,"G"));
a.signatures.push_back(CMutationSignature("TCC",2,"T"));
a.signatures.push_back(CMutationSignature("TCG",2,"T"));
a.signatures.push_back(CMutationSignature("TCC",2,"G"));
a.signatures.push_back(CMutationSignature("TCG",2,"G"));
a.ClassifyMutations(m,cancers,samples,&human);
a.CalculateAPOBECEnrichment(&human);
return 0;
CAllMotifs c;
c.AnalysisRTExp(string(RESULTS_FOLDER)+"/ALL",argv[1],argv[2]);
return 0;
time_t t;
tm* now;
// Start date/time
t = time(0); // get time now
now = localtime(&t);
cout << (now->tm_year + 1900) << '-' << (now->tm_mon + 1) << '-' << now->tm_mday << ' ' << now->tm_hour << ":" << now->tm_min << ":" << now->tm_sec << "\n";
//CHumanGenome human;
//human.InitializeHuman("37", HUMAN_PATH, ".fa", "FASTA");
/* CSignatureAnalysis a;
a.signatures.push_back(CMutationSignature("TCA",2,"T"));
a.signatures.push_back(CMutationSignature("TCT",2,"T"));
a.signatures.push_back(CMutationSignature("TCA",2,"G"));
a.signatures.push_back(CMutationSignature("TCT",2,"G"));
a.signatures.push_back(CMutationSignature("TCC",2,"T"));
a.signatures.push_back(CMutationSignature("TCG",2,"T"));
a.signatures.push_back(CMutationSignature("TCC",2,"G"));
a.signatures.push_back(CMutationSignature("TCG",2,"G"));
a.ClassifyMutations(&human);
return 0; */
/*
CMutations m;
int isHeader = 1;
m.LoadMutations(CANCER_MUTATIONS, isHeader);
CSignatureAnalysis a;
a.CalculateExpressionAllMotifs(m, "MOTIFS_EXP/ALLMUTS_in_EXPbins", &human, argv[1], argv[2]);
a.CalculateTargetsinExpBinAllMotifs("MOTIFS_EXP/ALLMOTIFS_in_EXPbins", &human, argv[1], argv[2]);
*/
// End date/time
t = time(0);
now = localtime(&t);
cout << (now->tm_year + 1900) << '-' << (now->tm_mon + 1) << '-' << now->tm_mday << ' ' << now->tm_hour << ":" << now->tm_min << ":" << now->tm_sec << "\n";
return 0;
//CAPOBEC a;
//a.RunAnalysis(argc, argv);
return 0;
}