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ARMADiLLO_main_quick.cpp
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#include <math.h>
#include <cstdlib>
#include <random>
#include <iostream>
#include <ctime>
#include <iomanip>
#include <sstream>
#include <vector>
#include <string>
#include <map>
#include <set>
#include <boost/algorithm/string.hpp>
#include "HTML.hpp"
#include "utilities.hpp"
#include <algorithm>
#include <boost/filesystem/operations.hpp>
//#include "boost/filesystem.hpp"
#include <fstream>
#include <sys/stat.h>
#include <sys/types.h>
#include <dirent.h>
#include <thread>
#include <mutex>
//#include <boost/filesystem/fstream.hpp>
//#define BOOST_FILESYSTEM_NO_DEPRECATED
#include <boost/optional.hpp>
using namespace std;
using namespace boost;
using namespace boost::filesystem;
//classes
class S5F_mut
{
public:
string fivemer, group, subst_group;
double score,score25,score75;
map<char, double> substitutions;
~S5F_mut(){};
S5F_mut(){};
S5F_mut(string _fivemer,double _score, string _group, double _score25, double _score75)
{
fivemer=_fivemer;
score=_score;
group=_group;
score25=_score25;
score75=_score75;
}
};
class Seq //nucleotide level sequence object (later could have each base point to a aa object)
{
public:
int aa_num;
string aa;
string base;
double S5F_mut_score;
double simulated_aa_positional_frequency;
string CDR_markup;
bool isMut;
map<char,double> all_simulated_aa_positional_frequencies_map;
string SMUA_code;
~Seq(){};
Seq(){};
Seq(string _base, int _aa_num,string _aa,double _S5F_mut_score)
{
base=_base;
aa_num=_aa_num;
aa=_aa;
S5F_mut_score=_S5F_mut_score;
}
};
///functions
void read_SMUA_file(string, vector<vector<string> > &);
void load_S5F_files(string,string, map<string,S5F_mut> &);
void process_fasta_sequence_to_seq_vector(string &,vector<Seq> &, map<string,string> &, map<string,S5F_mut> &);
void process_SMUA_sequence_to_seq_vector(string &, string &, vector<Seq> &, map<string,string> &, map<string, S5F_mut> &);
void convert_2D_seq_vector_to_HTML_table(vector<vector<Seq> >&, vector<string> &, HTML::Table &, double &);
void number_of_mutations_two_seqs(string &, string &, int &);
void simulate_S5F_mutation(string , int &, map<string,S5F_mut> &, mt19937 &, uniform_real_distribution<double> &, bool, vector<string> &, bool, vector<bool> &);
vector<pair<char,double> > sort_map_into_pair_vctr(map<char,double> &);
bool mycompare(pair<char,double> A, pair<char,double> B){return A.second > B.second;}
void correct_for_fivemer_with_gap(int, string, string &);
void print_output(string, vector<vector<Seq> > &, vector<string>, int, double);
void print_tile_view(string,vector<vector<Seq> > &, vector<string>, int, double, vector<double> &);
void print_pct_progress(int, int, int);
void get_mutability_scores(map<string,S5F_mut> &, string, int, bool, vector<bool> &, vector<double> &, vector<double> &, double &, double &);
void print_freq_table_to_file(string, map<int, map<char,double> > &);
void cleanup_SMUA_sequences(string, string, string , string , string , string &, string &, string &, string , string , int &, bool &);
bool sequence_has_ambiguities(string);
void convert_2D_seq_vector_to_HTML_table_for_tiles_view(vector<vector<Seq> >&, vector<string> &, HTML::Table &, double &, vector<double> &, int &);
void print_output_for_tiles_view(string, vector<vector<Seq> > &, vector<string>, int, double, vector<double> &);
void replace_UCA_sequence_in_SMUA(string, string, string, string, string &, string &, string &);
void read_V(const std::string &, map<string,map<int, map<char,double> >> &);
///templated functions
template <typename Type>
void vector2D_to_3D(vector<vector<Type> > &, int, vector<vector<vector<Type> > > &);
template <typename Type>
void vector1D_to_2D(vector<Type> &, int, vector<vector<Type> > &);
template <typename Type>
string convert_to_string(Type);
map<string, map<string, string> > J_genes_list();
///OLD TODO:
//0. The gap bases should have n/a for mutability score in HTML
//1. Use the markup string to highlight CDRs in the HTML
//2. Make sure last cell in ladder is 1 always
int main(int argc, char *argv[])
{
if (argc <2){cout << "USAGE: analyze_mutations -freq_dir [V, J Frequency file directory] -SMUA [SMUA file] -w [line wrap length (60)] -m [S5F mutability file] -s [S5F substitution file] -max_iter [cycles of B cell maturation(100)] -c [cutoff for highlighting low prob (1=1%)] -replace_J_upto [number of replacements in J allowed] -chain [chain type (heavy=default|kappa|lambda)] -species [(human=default|rhesus)] -clean_first [clean the SMUA prior to running] -output_seqs [output sim seqs] -random_seed [provide a random seed]\n"; exit(1);}
///get cmdline args
int i=0, line_wrap_length=60, max_iter=100, mutation_count_from_cmdline=-1, replace_J_upto=0, random_seed=0;
string freq_dir="", fasta_filename="", mutability_filename="", substitution_filename="", SMUA_filename="", species="human", chain_type="heavy", input_UCA_sequence="";
int SMUA_start=0, SMUA_end=-1;
double low_prob_cutoff=.02;
bool ignore_CDR3=false, clean_SMUA_first=false, user_provided_random_seed=false, remutate=false, output_seqs=false, quick=false;
while(i<argc)
{
string arg=argv[i];
string next_arg;
if (i<argc-1){next_arg=argv[i+1];}else{next_arg="";}
// if ((arg.substr(0,1)=="-")&&(next_arg.substr(0,1)=="-")){cerr << "incorrectly formatted cmdline\n"; exit(1);}
if (arg == "-SMUA")
{
SMUA_filename=next_arg;
}
if (arg == "-m")
{
mutability_filename=next_arg;
}
if (arg == "-s")
{
substitution_filename=next_arg;
}
if (arg == "-freq_dir")
{
freq_dir=next_arg;
quick=true;
}
if (arg == "-w")
{
line_wrap_length=atoi(next_arg.c_str());
}
if (arg == "-max_iter")
{
max_iter=atoi(next_arg.c_str());
}
if (arg == "-mut_count")
{
mutation_count_from_cmdline=atoi(next_arg.c_str());
}
if (arg == "-c")
{
low_prob_cutoff=atof(next_arg.c_str())/100.0;
}
if (arg == "-ignore_CDR3")
{
ignore_CDR3=true;
}
if (arg == "-start")
{
SMUA_start=atoi(next_arg.c_str());
}
if (arg == "-end")
{
SMUA_end=atoi(next_arg.c_str());
}
if (arg == "-replace_J_upto")
{
replace_J_upto=atoi(next_arg.c_str());
}
if (arg == "-species")
{
species=next_arg;
}
if (arg == "-chain")
{
chain_type=next_arg;
}
if (arg == "-clean_first")
{
clean_SMUA_first=true;
}
if (arg == "-random_seed")
{
random_seed=atoi(next_arg.c_str());
user_provided_random_seed=true;
}
if (arg == "-remutate")
{
bool remutate=true;
//cerr << "REMUTATE HAS NOT YET BEEN IMPLEMENTED. FEATURE COMING SOON!\n";
}
if (arg == "-output_seqs")
{
output_seqs=true;
}
if (arg == "-UCA_sequence")
{
input_UCA_sequence=next_arg;
}
i++;
}
cerr << "highlighting residues with less than " << low_prob_cutoff << " probability for mutation\n";
///amino acids vector
vector<char> amino_acids={'A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y'};
///setup random num generation
std::random_device rd;
int seed;
if (user_provided_random_seed)
{seed=random_seed;}
else
{seed=rd();}
std::mt19937 gen(seed);
std::uniform_real_distribution<double> dis(0, 1);
//define color ladder
vector<double> color_ladder{0.0001, 0.001, 0.01, 0.02, 0.10, 0.20, 0.5, 1};
///load dna_to_aa map
map<string,string> dna_to_aa_map;
get_aa_tranx_map(dna_to_aa_map);
///read input sequence alignment
map <string, string> sequences;
vector <string> sequence_names;
vector<vector<string> > SMUA_alignments_and_markup;
read_SMUA_file(SMUA_filename, SMUA_alignments_and_markup);
///load S5F files
map <string, S5F_mut> S5F_5mers;
load_S5F_files(mutability_filename,substitution_filename, S5F_5mers);
cout << "NAME\t#AA_MUTS\t#MUTS\t<.02\t<.01\t<.001\t<.0001\t#INS\t#DEL\t#INDELS/3\tCDR3_LEN\n";
const std::string direct=freq_dir;
map<string,map<int, map<char,double> >> v_input;
if (quick==true) {
std::mutex mtx;
ignore_CDR3=true;
mtx.lock();
read_V(direct, v_input);
mtx.unlock();
}
map<string, map<string, string> > J_genes=J_genes_list();
//iterate through the SMUA file and perform mutation analysis for each sequence
double total_elapsed_time=0;
if (SMUA_end==-1){SMUA_end=SMUA_alignments_and_markup.size();}
if (SMUA_end>SMUA_alignments_and_markup.size()){SMUA_end=SMUA_alignments_and_markup.size();}
//for(int i=0; i<SMUA_alignments_and_markup.size(); i++)
for(int i=SMUA_start; i<SMUA_end; i++)
{
clock_t begin=clock();
string sequence_name=SMUA_alignments_and_markup[i][0];
string sequence=SMUA_alignments_and_markup[i][1];
string UCA_sequence_name=SMUA_alignments_and_markup[i][2];
string UCA_sequence=SMUA_alignments_and_markup[i][3];
string markup_header=SMUA_alignments_and_markup[i][4];
string markup_string=SMUA_alignments_and_markup[i][5];
string new_sequence="", new_UCA_sequence="", new_markup_string="";
int number_of_replacements=0;
bool error_status=false;
if (clean_SMUA_first)
{
cerr << "Cleaning SMUA step\n";
cleanup_SMUA_sequences(sequence_name, markup_header, UCA_sequence, sequence, markup_string, new_UCA_sequence, new_sequence, new_markup_string, species, chain_type, number_of_replacements, error_status);
if (number_of_replacements>replace_J_upto)
{
cerr << "Sequence: " << sequence_name << " required " << number_of_replacements << " replacements at the end of the J where " << replace_J_upto << " is allowed (user defined). Skipping that sequence\n";
cout << sequence_name << "\tN/A\tN/A\tN/A\tN/A\tN/A\tN/A\tN/A\tN/A\tN/A\n";
continue;
}
if (error_status){
cerr << "SMUA incorrectly formatted for sequence " << sequence_name << ". Skipping that sequence\n";
cout << sequence_name << "\tN/A\tN/A\tN/A\tN/A\tN/A\tN/A\tN/A\tN/A\tN/A\n";
continue;
}
UCA_sequence=new_UCA_sequence;
sequence=new_sequence;
markup_string=new_markup_string;
}
if (input_UCA_sequence!="")//replace all UCAs with input UCA
{
new_UCA_sequence="", new_sequence="", new_markup_string="";
replace_UCA_sequence_in_SMUA(sequence, UCA_sequence, markup_string, input_UCA_sequence, new_sequence, new_UCA_sequence, new_markup_string);
UCA_sequence=new_UCA_sequence;
sequence=new_sequence;
markup_string=new_markup_string;
// cout << UCA_sequence << "\n" << sequence << "\n" << markup_string << "\n";
}
string output_filename=sequence_name+".ARMADiLLO.html";
string tiles_output_filename=sequence_name+".tiles.html";
vector<bool> V_gene_mark(markup_string.length(), false);
int V_gene_counter=0, J_gene_counter=0;
string UCA_V="", seq_V="",UCA_J="", seq_J="",markup_string_V="",UCA_other="", seq_other="", markup_string_other="";
//read in V gene;
if (quick==true) {
//read_V(direct, v_input);
char * ptr;
char * buf=const_cast<char *>(markup_string.c_str());
int ch = '3';
ptr = strrchr( buf, ch );
int leng = markup_string.length()-strlen(ptr)+1;
for(int j=0; j<markup_string.length(); j++)
{
if (j<leng)
{
V_gene_mark[j]=true;
V_gene_counter++;
UCA_V+=UCA_sequence[j];
seq_V+=sequence[j];
markup_string_V+=markup_string[j];
}
else
{
V_gene_mark[j]=false;
UCA_other+=UCA_sequence[j];
seq_other+=sequence[j];
markup_string_other+=markup_string[j];
}
}
}
vector<bool> shield_mutations_other(markup_string_other.length(), false);
int shield_counter_other=0;
string UCA_CDR3_other="", seq_CDR3_other="";
for(int j=0; j<markup_string_other.length(); j++)
{
if ((markup_string_other[j]=='V')||(markup_string_other[j]=='n')||(markup_string_other[j]=='D')||(markup_string_other[j]=='J'))
{
shield_mutations_other[j]=true;
shield_counter_other++;
UCA_CDR3_other+=UCA_other[j];
seq_CDR3_other+=seq_other[j];
}
else
{
shield_mutations_other[j]=false;
}
}
int J_start;
J_start=shield_counter_other+V_gene_counter;
J_gene_counter=sequence.length()-J_start;
UCA_J=UCA_sequence.substr(J_start,J_gene_counter);
seq_J=sequence.substr(J_start,J_gene_counter);
//if CDR3 is to be ignored, get CDR3 bases from markup string and store in bool vector
vector<bool> shield_mutations(markup_string.length(), false);
int shield_counter=0;
string UCA_CDR3="", seq_CDR3="";
for(int j=0; j<markup_string.length(); j++)
{
if ((markup_string[j]=='V')||(markup_string[j]=='n')||(markup_string[j]=='D')||(markup_string[j]=='J'))
{
shield_mutations[j]=true;
shield_counter++;
UCA_CDR3+=UCA_sequence[j];
seq_CDR3+=sequence[j];
}
else
{
shield_mutations[j]=false;
}
}
if (ignore_CDR3){cerr << "Shielding CDR3 from mutation. CDR3 has " << shield_counter << " bases, mutability zeroed out for these\n"; }
int CDR3_length=shield_counter;
int mut_count=0, CDR3_mut_count=0, other_mut_count=0, V_mut_count=0, J_mut_count=0;
int aa_mut_count=0, CDR3_aa_mut_count=0, V_aa_mut_count, other_aa_mut_count, J_aa_mut_count;
string UCA_aa_sequence="", aa_sequence="", UCA_aa_CDR3="", seq_aa_CDR3="",UCA_aa_V="", seq_aa_V="", UCA_aa_J="", seq_aa_J="",UCA_aa_other="", seq_aa_other="";
vector<Seq> seq_vector, UCA_seq_vector, aa_seq_vector, aa_UCA_seq_vector;
process_SMUA_sequence_to_seq_vector(sequence, markup_string, seq_vector, dna_to_aa_map, S5F_5mers);
process_SMUA_sequence_to_seq_vector(UCA_sequence, markup_string, UCA_seq_vector, dna_to_aa_map, S5F_5mers);
//calc number of dna mutations
number_of_mutations_two_seqs(UCA_sequence, sequence, mut_count);
number_of_mutations_two_seqs(UCA_CDR3, seq_CDR3, CDR3_mut_count); //get mut count for CDR3
//calc number of amino acid mutations
translate_dna_to_aa(UCA_sequence, UCA_aa_sequence, 1, dna_to_aa_map);
translate_dna_to_aa(sequence, aa_sequence, 1, dna_to_aa_map);
translate_dna_to_aa(seq_CDR3, seq_aa_CDR3, 1, dna_to_aa_map);
translate_dna_to_aa(UCA_CDR3, UCA_aa_CDR3, 1, dna_to_aa_map);
number_of_mutations_two_seqs(UCA_aa_sequence, aa_sequence, aa_mut_count);
number_of_mutations_two_seqs(UCA_aa_CDR3, seq_aa_CDR3, CDR3_aa_mut_count);
map<int, map<char,double> > mature_mutant_positional_aa_freqs1, positional_aa_freqs1;
if (quick==true) {
number_of_mutations_two_seqs(UCA_other, seq_other, other_mut_count); //get mut count for other
number_of_mutations_two_seqs(UCA_V, seq_V, V_mut_count);
number_of_mutations_two_seqs(UCA_J, seq_J, J_mut_count);
translate_dna_to_aa(seq_V, seq_aa_V, 1, dna_to_aa_map);
translate_dna_to_aa(UCA_V, UCA_aa_V, 1, dna_to_aa_map);
translate_dna_to_aa(seq_other, seq_aa_other, 1, dna_to_aa_map);
translate_dna_to_aa(UCA_other, UCA_aa_other, 1, dna_to_aa_map);
translate_dna_to_aa(seq_J, seq_aa_J, 1, dna_to_aa_map);
translate_dna_to_aa(UCA_J, UCA_aa_J, 1, dna_to_aa_map);
number_of_mutations_two_seqs(UCA_aa_V, seq_aa_V, V_aa_mut_count);
number_of_mutations_two_seqs(UCA_aa_other, seq_aa_other, other_aa_mut_count);
number_of_mutations_two_seqs(UCA_aa_J, seq_aa_J, J_aa_mut_count);
std::string str("IGHV");
std::string str1("|");
std::size_t found0=markup_header.find(str);
std::size_t found1=markup_header.find(str1);
std::size_t found2=markup_header.find(str1,found1+1);
string UCA_sequence_name1=markup_header.substr(found0,found2-found0);
V_mut_count=round((mut_count*seq_V.length()/(sequence.length()-shield_counter)+V_mut_count*3)/4);
string freq_table=UCA_sequence_name1+"_"+std::to_string(V_mut_count)+".freq_table.txt";
cerr<<"Sequence name"<<markup_header<<'\n';
cerr << "Chosen V frequency table"<<freq_table<<"\n";
string shift=UCA_aa_sequence;
for (int i=0; i < UCA_aa_sequence.length(); i++){
if (UCA_sequence[3*i]=='-' || UCA_sequence[3*i+1]=='-' || UCA_sequence[3*i+2]=='-') {
shift[i]='1';
} else {
shift[i]='0';
}
if (sequence[3*i]=='-' || sequence[3*i+1]=='-' || sequence[3*i+2]=='-') {
shift[i]='0';
}
}
///get positional frequency of aa from simulated sequences (with same num maturation mutations)
positional_aa_freqs1=v_input.find(freq_table)->second;
///dealing with insertion and deletion
int cnt=0 ;
for(int j=0; j<seq_V.length()/3; j++)
{
if (j>0 && shift[j-1]=='1' ) {
cnt+=1;
}
for(int k=0; k<amino_acids.size(); k++)
{
mature_mutant_positional_aa_freqs1[j][amino_acids[k]]=positional_aa_freqs1[j-cnt][amino_acids[k]];
}
}
for(int j=0; j<seq_CDR3.length()/3; j++) {
for(int k=0; k<amino_acids.size(); k++)
{
if (amino_acids[k]==seq_aa_CDR3[j]) {
if (UCA_aa_CDR3[j]==seq_aa_CDR3[j]) {
mature_mutant_positional_aa_freqs1[j+seq_V.length()/3][amino_acids[k]]=1.0;
} else {
mature_mutant_positional_aa_freqs1[j+seq_V.length()/3][amino_acids[k]]=0.0;
}
} else {
mature_mutant_positional_aa_freqs1[j+seq_V.length()/3][amino_acids[k]]=0.0;
}
}
}
std::string str2("IGHJ");
found0=markup_header.find(str2);
UCA_sequence_name1=markup_header.substr(found0,markup_header.length()-found0);
J_mut_count=round((mut_count*seq_J.length()/(sequence.length()-shield_counter)+J_mut_count*3)/4);
freq_table=UCA_sequence_name1+"_"+std::to_string(J_mut_count)+".freq_table.txt";
cerr << "Chosen J frequency table:" << freq_table<<"\n";
if (J_mut_count==0) {
for(int j=0; j<UCA_J.length()/3; j++)
{
for(int k=0; k<amino_acids.size(); k++)
{
if (amino_acids[k]==seq_aa_J[j]) {
if (UCA_aa_J[j]==seq_aa_J[j]) {
mature_mutant_positional_aa_freqs1[j+J_start/3][amino_acids[k]]=1.0;
} else {
mature_mutant_positional_aa_freqs1[j+J_start/3][amino_acids[k]]=0.0;
}
} else {
mature_mutant_positional_aa_freqs1[j+J_start/3][amino_acids[k]]=0.0;
}
}
}
} else {
positional_aa_freqs1=v_input.find(freq_table)->second;
int cnt=0 ;
for(int j=0; j<seq_J.length()/3; j++)
{
if (j>0 && shift[J_start/3+j-1]=='1' ) {
cnt+=1;
}
for(int k=0; k<amino_acids.size(); k++)
{
mature_mutant_positional_aa_freqs1[J_start/3+j][amino_acids[k]]=positional_aa_freqs1[j-cnt][amino_acids[k]];
}
}
}
if (ignore_CDR3)
{
mut_count-=CDR3_mut_count;
aa_mut_count-=CDR3_aa_mut_count;
other_mut_count-=CDR3_mut_count;
other_aa_mut_count-=CDR3_aa_mut_count;
}
other_mut_count=round((mut_count*seq_other.length()/(sequence.length()-shield_counter_other)+3*other_mut_count)/4);
} else {
if (ignore_CDR3)
{
mut_count-=CDR3_mut_count;
aa_mut_count-=CDR3_aa_mut_count;
cerr << "ignoring " << CDR3_mut_count << " mutations\n" ;
}
}
cerr << "processing " << sequence_name << " which has " << mut_count << " mutations\n";
//check for any UCA weirdness
//cout << sequence_name << "\n" << sequence << "\n" << UCA_sequence << "\n" << markup_string << "\n";
if (dna_sequence_has_stop_codon_in_reading_frame(UCA_sequence))
{
cerr << "germline has stop codon...skipping this sequence\n";
cout << sequence_name << "\tN/A\tN/A\tN/A\tN/A\tN/A\tN/A\tN/A\tN/A\tN/A\tN/A\n";
continue;
}
//number of indels
int insertion_count=0, deletion_count=0;
for(int j=0; j<UCA_sequence.length(); j++)
{
if (UCA_sequence[j] == '-'){insertion_count++;}
if (sequence[j] == '-'){deletion_count++;}
}
//simulate maturation at mutation frequency = to observed
vector<string> mature_mutant_sequences;
map<int, map<char,double> > mature_mutant_positional_aa_freqs;
if (quick==false) {
cerr << "Simulating maturation...\n";
for(int j=1; j<=max_iter; j++)
{
print_pct_progress(j, max_iter, 1);
vector<string> mutant_sequences;
simulate_S5F_mutation(UCA_sequence, mut_count, S5F_5mers, gen, dis,true, mutant_sequences, ignore_CDR3, shield_mutations);
string aa_sequence;
translate_dna_to_aa(mutant_sequences[mutant_sequences.size()-1], aa_sequence, 1, dna_to_aa_map);
mature_mutant_sequences.push_back(aa_sequence);
}
cerr << "done\n";
///get positional frequency of aa from simulated sequences (with same num maturation mutations)
///init map to 0
for(int j=0; j<mature_mutant_sequences[0].length(); j++)
{
for(int k=0; k<amino_acids.size(); k++)
{
mature_mutant_positional_aa_freqs[j][amino_acids[k]]=0;
}
}
for(int j=0; j<mature_mutant_sequences.size(); j++)
{
//cout << ">mutant" << i+1 << "\n" << mature_mutant_sequences[i] << "\n";
for(int k=0; k<mature_mutant_sequences[j].length(); k++)
{
mature_mutant_positional_aa_freqs[k][mature_mutant_sequences[j][k]]+=(1/(double)mature_mutant_sequences.size());
}
}
}
//output simulated seqs if necessary
if (output_seqs)
{
string seqs_fasta_file=sequence_name+".ARMADiLLO.simulated_seqs.fasta";
ofstream file_out;
file_out.open(seqs_fasta_file.c_str());
for(int j=0; j<mature_mutant_sequences.size(); j++)
{
file_out << ">seq_" << j+1 << "\n";
file_out << mature_mutant_sequences[j] << "\n";
}
file_out.close();
}
if (quick==true) {
mature_mutant_positional_aa_freqs=mature_mutant_positional_aa_freqs1;
}
///annotate seq vector with positional aa freq
for(int j=0; j<seq_vector.size(); j++) //per position
{
if ((UCA_seq_vector[j].base == "-") || (seq_vector[j].base== "-")) //indel special case
{
seq_vector[j].simulated_aa_positional_frequency=-99.99;
}
else
{
seq_vector[j].simulated_aa_positional_frequency=mature_mutant_positional_aa_freqs[seq_vector[j].aa_num-1][seq_vector[j].aa[0]];
}
seq_vector[j].all_simulated_aa_positional_frequencies_map=mature_mutant_positional_aa_freqs[seq_vector[j].aa_num-1];
}
///tabulate
int p02_count=0, p01_count=0, p001_count=0, p0001_count=0;
map<string, int> region_counts;
//cerr << seq_vector.size() << "\t" << UCA_seq_vector.size() << "\n";
for(int j=0; j<seq_vector.size(); j+=3)
{
// cerr << "j: " << j << "\n";
if ((UCA_seq_vector[j].aa=="-")||(UCA_seq_vector[j].base=="-")){continue;} //skip if insertion i.e. gap in UCA_seq sequence
if (j+1<seq_vector.size()){if(UCA_seq_vector[j+1].base=="-"){continue;}}
if (j+2<seq_vector.size()){if(UCA_seq_vector[j+2].base=="-"){continue;}}
if ((seq_vector[j].aa=="-")||(seq_vector[j].base=="-")){continue;} //skip if insertion i.e. gap in obs sequence
if (j+1<seq_vector.size()){if(seq_vector[j+1].base=="-"){continue;}}
if (j+2<seq_vector.size()){if(seq_vector[j+2].base=="-"){continue;}}
if (shield_mutations[j]){continue;}
if (seq_vector[j].simulated_aa_positional_frequency<.02){p02_count++;}
if (seq_vector[j].simulated_aa_positional_frequency<.01){p01_count++;}
if (seq_vector[j].simulated_aa_positional_frequency<.001){p001_count++;}
if (seq_vector[j].simulated_aa_positional_frequency<.0001){p0001_count++;}
}
if (mut_count==0)
{
cerr << "0 mutations found\n";
cout << sequence_name << "\t" << aa_mut_count << "\t" << mut_count << "\t" << 0 << "\t" << 0 << "\t" << 0 << "\t" << 0 << "\t" << insertion_count << "\t" << deletion_count << "\t" << (insertion_count+deletion_count)/3 << "\t" << CDR3_length << "\n";
}
else
{
cout << sequence_name << "\t" << aa_mut_count << "\t" << mut_count << "\t" << p02_count << "\t" << p01_count << "\t" << p001_count << "\t" << p0001_count << "\t" << insertion_count << "\t" << deletion_count << "\t" << (insertion_count+deletion_count)/3 << "\t" << CDR3_length << "\n";
///print detailed ARMADiLLO output as HTML
vector<vector<Seq> > all_sequences;
all_sequences.push_back(UCA_seq_vector);
all_sequences.push_back(seq_vector);
vector<string> sequence_names;
sequence_names.push_back(UCA_sequence_name);
sequence_names.push_back(sequence_name);
print_output(output_filename, all_sequences, sequence_names, line_wrap_length, low_prob_cutoff);
///print tiles as HTML
for(int j=0; j<seq_vector.size(); j+=3)
{
if (seq_vector[j].aa != UCA_seq_vector[j].aa){seq_vector[j].isMut=true;}else{seq_vector[j].isMut=false;}
UCA_seq_vector[j].isMut=false;
UCA_seq_vector[j].simulated_aa_positional_frequency=1;
aa_UCA_seq_vector.push_back(UCA_seq_vector[j]);
aa_seq_vector.push_back(seq_vector[j]);
}
vector<vector<Seq> > all_aa_sequences;
vector<string> aa_sequence_names;
all_aa_sequences.push_back(aa_UCA_seq_vector);
all_aa_sequences.push_back(aa_seq_vector);
aa_sequence_names.push_back("UCA");
aa_sequence_names.push_back(sequence_name);
//comment out the below line for running on linux, however, runs well without comment out on mac.
//print_output_for_tiles_view(tiles_output_filename, all_aa_sequences, aa_sequence_names, line_wrap_length, low_prob_cutoff, color_ladder);
}
string output_freq_table=sequence_name+".freq_table.txt";
print_freq_table_to_file(output_freq_table,mature_mutant_positional_aa_freqs);
clock_t end=clock();
double elapsed_secs = double(end - begin) / CLOCKS_PER_SEC;
cerr << "TIME: " << sequence_name << " took " << elapsed_secs << " to process\n";
total_elapsed_time+=elapsed_secs;
}
cerr << "TOTAL ELAPSED TIME: " << total_elapsed_time << "\n";
return 0;
}
void read_V(const std::string & name, map<string,map<int, map<char,double> >> & v_input) {
vector<char> amino_acids={'A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y'};
//path p("/Users/yw328/Documents/My_Scripts/Kevin-prog/ARMADiLLO/freq_table");
DIR *dpdf= opendir(name.c_str());
struct dirent *epdf;
struct stat filestat;
map<int, map<char,double> > mature_mutant_positional_aa_freqs1;
clock_t begin=clock();
cerr <<"Loading, Please wait ......";
//dpdf = opendir(direct);
if (dpdf != NULL){
while ((epdf = readdir(dpdf))){
map<int, map<char,double> > mature_mutant_positional_aa_freqs;
string Vgen = name+'/'+ epdf->d_name;
if (stat( Vgen.c_str(), &filestat )) continue;
if (S_ISDIR( filestat.st_mode )) continue;
ifstream file(Vgen, std::ios::in );
string dummyline;
if (!file.is_open()) {cerr << "could not open " << epdf->d_name << " ...exiting...\n"; exit(1);}
getline(file, dummyline);
int pos1; int pos=0; double A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y;
while ((!getline(file, dummyline).eof())) {
//file >>pos1>>comma>>A>>comma>>C>>comma>>D>>comma>>E>>comma>>F>>comma>>G>>comma>>H>>I>>comma>>K>>comma>>L>>comma>>M>>comma>>N>>comma>>P>>comma>>Q>>comma>>R>>comma>>S>>comma>>T>>comma>>V>>comma>>W>>comma>>Y;
//cout <<dummyline<<'\n';
//cerr<<dummyline.length()<<'\n';
istringstream ss(dummyline);
getline(ss,dummyline,',')>>A;
getline(ss,dummyline,',')>>C;
getline(ss,dummyline,',')>>D;
getline(ss,dummyline,',')>>E;
getline(ss,dummyline,',')>>F;
getline(ss,dummyline,',')>>G;
getline(ss,dummyline,',')>>H;
getline(ss,dummyline,',')>>I;
getline(ss,dummyline,',')>>K;
getline(ss,dummyline,',')>>L;
getline(ss,dummyline,',')>>M;
getline(ss,dummyline,',')>>N;
getline(ss,dummyline,',')>>P;
getline(ss,dummyline,',')>>Q;
getline(ss,dummyline,',')>>R;
getline(ss,dummyline,',')>>S;
getline(ss,dummyline,',')>>T;
getline(ss,dummyline,',')>>V;
getline(ss,dummyline,',')>>W;
getline(ss,dummyline,',')>>Y;
mature_mutant_positional_aa_freqs[pos][amino_acids[0]]=A;
mature_mutant_positional_aa_freqs[pos][amino_acids[1]]=C;
mature_mutant_positional_aa_freqs[pos][amino_acids[2]]=D;
mature_mutant_positional_aa_freqs[pos][amino_acids[3]]=E;
mature_mutant_positional_aa_freqs[pos][amino_acids[4]]=F;
mature_mutant_positional_aa_freqs[pos][amino_acids[5]]=G;
mature_mutant_positional_aa_freqs[pos][amino_acids[6]]=H;
mature_mutant_positional_aa_freqs[pos][amino_acids[7]]=I;
mature_mutant_positional_aa_freqs[pos][amino_acids[8]]=K;
mature_mutant_positional_aa_freqs[pos][amino_acids[9]]=L;
mature_mutant_positional_aa_freqs[pos][amino_acids[10]]=M;
mature_mutant_positional_aa_freqs[pos][amino_acids[11]]=N;
mature_mutant_positional_aa_freqs[pos][amino_acids[12]]=P;
mature_mutant_positional_aa_freqs[pos][amino_acids[13]]=Q;
mature_mutant_positional_aa_freqs[pos][amino_acids[14]]=R;
mature_mutant_positional_aa_freqs[pos][amino_acids[15]]=S;
mature_mutant_positional_aa_freqs[pos][amino_acids[16]]=T;
mature_mutant_positional_aa_freqs[pos][amino_acids[17]]=V;
mature_mutant_positional_aa_freqs[pos][amino_acids[18]]=W;
mature_mutant_positional_aa_freqs[pos][amino_acids[19]]=Y;
//cerr<<mature_mutant_positional_aa_freqs[pos][nucleotides[0]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[1]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[2]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[3]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[4]]<<mature_mutant_positional_aa_freqs[pos][nucleotides[5]]<<mature_mutant_positional_aa_freqs[pos][nucleotides[6]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[7]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[8]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[9]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[10]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[11]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[12]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[13]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[14]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[15]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[16]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[17]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[18]]<<' '<<mature_mutant_positional_aa_freqs[pos][nucleotides[19]]<<'\n';
//cerr<<pos<<' '<<'\n';
pos++;
}
file.close();
//string output_freq_table="temp.freq_table.txt";
//print_freq_table_to_file(output_freq_table,mature_mutant_positional_aa_freqs);
//map<string,map<int, map<char,double> >> temp;
string tem=epdf->d_name;
//temp.insert({tem,mature_mutant_positional_aa_freqs});
//temp[tem]=mature_mutant_positional_aa_freqs;
v_input[tem]=mature_mutant_positional_aa_freqs;
// v_input.push_back(temp);
/* cerr<<" ";
cerr<<epdf->d_name<<'\n';
mature_mutant_positional_aa_freqs1=mature_mutant_positional_aa_freqs;
*/
// mature_mutant_positional_aa_freqs1=v_input[tem];
// std::cout << epdf->d_name << std::endl;
}
}
closedir(dpdf);
clock_t end=clock();
double elapsed_secs = double(end - begin) / CLOCKS_PER_SEC;
cerr << "Reading in files took " << elapsed_secs << " to process\n";
return ;
}
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
///
/// FUNCTION DEFINITIONS
///
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
void print_output_for_tiles_view(string filename, vector<vector<Seq> > &all_sequences, vector<string> sequence_names, int line_wrap_length, double low_prob_cutoff, vector<double> &color_ladder)
{
vector<vector<vector<Seq> > > split_all_sequences;
vector2D_to_3D(all_sequences,line_wrap_length, split_all_sequences);
///output html header
string file_string="";
file_string+="<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en'>\n";
file_string+="<head>\n";
file_string+=" <meta http-equiv='Content-Type' content='text/html; charset=utf-8' />\n";
file_string+=" <title>Antibody Mutation Analysis</title>\n";
file_string+=" <link rel='stylesheet' href='sequence_color.css' />\n";
file_string+="</head>\n";
file_string+="<body>\n";
file_string+="<p></p><br>\n";
//cerr << "number of splits: " << split_all_sequences.size() << "\n";
//for each split, make a HTML table and print it
int counter=1;
for(int i=0; i<split_all_sequences.size(); i++)
{
HTML::Table html_table;
html_table.hclass="results";
//convert seq vector to html table
cerr<<"fei"<<i;
convert_2D_seq_vector_to_HTML_table_for_tiles_view(split_all_sequences[i],sequence_names,html_table, low_prob_cutoff, color_ladder, counter);
cerr<<"fei1";
//missing step: stylize the table
//print HTML tables
html_table.print(file_string);
file_string+="<p></p>\n";
}
file_string+="<p><br></p><p align=\"center\"><img src=\"Mutation_Probability_legend.png\" alt=\"Mutation Probability Legend\" height=\"25\"></p>\n";
file_string+="</body>\n</html>\n";
ofstream file_out;
file_out.open(filename.c_str());
file_out << file_string;
file_out.close();
}
void print_freq_table_to_file(string filename, map<int, map<char,double> > &positional_aa_freqs)
{
ofstream file_out;
file_out.open(filename.c_str());
///amino acids vector
vector<char> amino_acids={'A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y'};
file_out << "pos";
for(int i=0; i<amino_acids.size(); i++){file_out << "," << amino_acids[i];}
file_out << "\n";
for(int j=0; j<positional_aa_freqs.size(); j++)
{
file_out << j+1;
for(int i=0; i<amino_acids.size(); i++)
{
file_out << "," <<positional_aa_freqs[j][amino_acids[i]];
}
file_out << "\n";
}
file_out.close();
}
void print_output(string filename, vector<vector<Seq> > &all_sequences, vector<string> sequence_names, int line_wrap_length, double low_prob_cutoff)
{
vector<vector<vector<Seq> > > split_all_sequences;
vector2D_to_3D(all_sequences,line_wrap_length, split_all_sequences);
///output html header
string file_string="";
file_string+="<html xmlns='http://www.w3.org/1999/xhtml' xml:lang='en'>\n";
file_string+="<head>\n";
file_string+=" <meta http-equiv='Content-Type' content='text/html; charset=utf-8' />\n";
file_string+=" <title>Antibody Mutation Analysis</title>\n";
file_string+=" <link rel='stylesheet' href='AMA.css' />\n";
file_string+="</head>\n";
file_string+="<body>\n";
file_string+="<p></p><br>\n";
//cerr << "number of splits: " << split_all_sequences.size() << "\n";
//for each split, make a HTML table and print it
for(int i=0; i<split_all_sequences.size(); i++)
{