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CASEclusters.cpp
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//
// CASEclusters.cpp
// APOBECXP
//
// Created by Marat Kazanov on 07/02/2020.
// Copyright © 2020 Marat Kazanov. All rights reserved.
//
#include "CASEclusters.hpp"
#include <map>
#include "mutation.hpp"
#include "replicationtime.hpp"
#include "options.h"
#include "expression.hpp"
#include "signanalysis.hpp"
void ProcessClusters()
{
// Genome
CHumanGenome human;
human.InitializeHuman("37", HUMAN_PATH, ".fa", "FASTA");
// Replication timing data
string path;
//CReplicationTiming rtIMR90;
//CReplicationTiming rtMCF7;
//CReplicationTiming rtNHEK;
CReplicationTiming rtHELA3;
//path = string(REPLICATION_TIMING_FOLDER)+string("/wgEncodeUwRepliSeqImr90WaveSignalRep1.mybed");
//rtIMR90.LoadReplicationTiming(path.c_str(), 0);
//rtIMR90.ReplicationStrand();
//path = string(REPLICATION_TIMING_FOLDER)+string("/wgEncodeUwRepliSeqMcf7WaveSignalRep1.mybed");
//rtMCF7.LoadReplicationTiming(path.c_str(), 0);
//rtMCF7.ReplicationStrand();
//path = string(REPLICATION_TIMING_FOLDER)+string("/wgEncodeUwRepliSeqNhekWaveSignalRep1.mybed");
//rtNHEK.LoadReplicationTiming(path.c_str(), 0);
//rtNHEK.ReplicationStrand();
path = string(REPLICATION_TIMING_FOLDER)+string("/wgEncodeUwRepliSeqHelas3WaveSignalRep1.mybed");
rtHELA3.LoadReplicationTiming(path.c_str(), 0);
rtHELA3.ReplicationStrand();
map<string,CReplicationTiming*> rtmap;
//rtmap["BLCA"] = &rtNHEK;
//rtmap["BRCA"] = &rtMCF7;
//rtmap["HNSC"] = &rtNHEK;
//rtmap["LUAD"] = &rtIMR90;
//rtmap["LUSC"] = &rtIMR90;
rtmap["CESC"] = &rtHELA3;
//rtIMR90.bins.push_back(CRTBin(0,-100,13.0766));
//rtIMR90.bins.push_back(CRTBin(1,13.0766,28.3851));
//rtIMR90.bins.push_back(CRTBin(2,28.3851,40.2474));
//rtIMR90.bins.push_back(CRTBin(3,40.2474,52.0254));
//rtIMR90.bins.push_back(CRTBin(4,52.0254,64.7194));
//rtIMR90.bins.push_back(CRTBin(5,64.7194,75.0635));
//rtIMR90.bins.push_back(CRTBin(6,75.0635,90.1735));
//rtMCF7.bins.push_back(CRTBin(0,-100,19.8872));
//rtMCF7.bins.push_back(CRTBin(1,19.8872,30.5993));
//rtMCF7.bins.push_back(CRTBin(2,30.5993,40.0364));
//rtMCF7.bins.push_back(CRTBin(3,40.0364,50.556));
//rtMCF7.bins.push_back(CRTBin(4,50.556,60.3904));
//rtMCF7.bins.push_back(CRTBin(5,60.3904,68.9953));
//rtMCF7.bins.push_back(CRTBin(6,68.9953,86.4342));
//rtNHEK.bins.push_back(CRTBin(0,-100,22.622));
//rtNHEK.bins.push_back(CRTBin(1,-100,32.1929));
//rtNHEK.bins.push_back(CRTBin(2,-100,41.1202));
//rtNHEK.bins.push_back(CRTBin(3,-100,50.9531));
//rtNHEK.bins.push_back(CRTBin(4,-100,59.6393));
//rtNHEK.bins.push_back(CRTBin(5,-100,67.2079));
//rtNHEK.bins.push_back(CRTBin(6,-100,80.7682));
rtHELA3.bins.push_back(CRTBin(0,-100,19.0528));
rtHELA3.bins.push_back(CRTBin(1,19.0528,32.8395));
rtHELA3.bins.push_back(CRTBin(2,32.8395,44.6798));
rtHELA3.bins.push_back(CRTBin(3,44.6798,55.0382));
rtHELA3.bins.push_back(CRTBin(4,55.0382,63.9244));
rtHELA3.bins.push_back(CRTBin(5,63.9244,71.6868));
rtHELA3.bins.push_back(CRTBin(6,71.6868,85.2286));
// Expression data
map<string,CExpression*> expmap;
CExpression blca,brca,hnsc,luad,lusc,cesc;
//blca.LoadExpression(string(EXPRESSION_FOLDER)+"/unpivot_expression_BLCA.txt");
//brca.LoadExpression(string(EXPRESSION_FOLDER)+"/unpivot_expression_BRCA.txt");
//hnsc.LoadExpression(string(EXPRESSION_FOLDER)+"/unpivot_expression_HNSC.txt");
//luad.LoadExpression(string(EXPRESSION_FOLDER)+"/unpivot_expression_LUAD.txt");
//lusc.LoadExpression(string(EXPRESSION_FOLDER)+"/unpivot_expression_LUSC.txt");
cesc.LoadExpression(string(EXPRESSION_FOLDER)+"/unpivot_expression_CESC.txt");
//expmap["BLCA"] = &blca;
//expmap["BRCA"] = &brca;
//expmap["HNSC"] = &hnsc;
//expmap["LUAD"] = &luad;
//expmap["LUSC"] = &lusc;
expmap["CESC"] = &cesc;
vector<CExpressionBin> expBins;
expBins.push_back(CExpressionBin(0,-9999999,0));
expBins.push_back(CExpressionBin(1,0,25));
expBins.push_back(CExpressionBin(2,25,100));
expBins.push_back(CExpressionBin(3,100,300));
expBins.push_back(CExpressionBin(4,300,550));
expBins.push_back(CExpressionBin(5,550,1000));
expBins.push_back(CExpressionBin(6,1000,2000));
expBins.push_back(CExpressionBin(7,2000,99999999999));
// Load genes
CHumanGenes genes;
genes.LoadGenes(string(HUMAN_GENES));
genes.PrepareForSearch();
// Load mutations
CMutations m;
vector<string> cancers;
vector<string> samples;
m.LoadMutations(FILE_FORMAT_FRIDRIKSSON,
"/Users/mar/BIO/PROJECTS/APOBEC/Project1_TranscriptionLevel/cluster/cluster_muts_CESC.csv",
cancers,samples,1,&human);
m.RenameSamples("/Users/mar/BIO/PROJECTS/PCAWG_APOBEC/PCAWG_samples_list.csv",2,3,16);
CMutation* mut;
int bin;
int strand;
int strandInconsistence;
for(int i=0;i<m.mutations.size();i++)
{
mut = &m.mutations[i];
rtmap[string(mut->cancer)]->GetRTBinStrand(rtmap,(*mut),bin,strand);
mut->RTbin = bin;
mut->RTstrand = strand;
bin = (*expmap[string(mut->cancer)]).GetExpressionBin(string(mut->sample), mut->chr, mut->pos, mut->isForwardStrand, genes, expBins, strand, strandInconsistence);
mut->EXPbin = bin;
mut->EXPstrand = strand;
}
m.SaveToFileRTExp("/Users/mar/BIO/PROJECTS/APOBEC/Project1_TranscriptionLevel/cluster/cluster_muts_processed_CESC.csv");
}
void MakeApobecMutationsFile()
{
// Genome
CHumanGenome human;
human.InitializeHuman("37", HUMAN_PATH, ".fa", "FASTA");
// Load mutations
CMutations m;
vector<string> cancers;
vector<string> samples;
m.LoadMutations(FILE_FORMAT_FRIDRIKSSON,
"/Users/mar/BIO/PROJECTS/APOBEC/Project1_TranscriptionLevel/cluster/cluster_muts_CESC.csv",
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"));
m.FilterMutations(a.signatureMuts,a.signatures,human,cancers,samples,&a.otherMuts);
a.signatureMuts.SaveToFile("/Users/mar/BIO/PROJECTS/APOBEC/Project1_TranscriptionLevel/cluster/mutations_apobec_CESC.tsv");
}