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Copy pathpreprocess.cpp
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166 lines (139 loc) · 6.17 KB
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#include "argument_parser.h"
#include "preprocess.h"
#include <algorithm>
#include <assert.h>
#include <cstring>
#include <filesystem>
#include <fstream>
#include <iostream>
#include <limits>
#include <stdlib.h>
#include <sstream>
#include <string>
#include <sys/stat.h>
#include <vector>
bool preprocess::file_setup(ArgumentParser& user_args){
// create output directory if it doesn't already exist
std::string cmd {"mkdir -p " + user_args.args["-o"] + "/intermediate_output/"};
system(cmd.c_str());
return true;
}
/* Checks that the user input all required flags */
bool preprocess::check_args(ArgumentParser& user_args){
// check required flags
std::list<std::string> preprocess_required {"-o", "--graph", "--tumor-ids", "--reference", "--read-sep"};
if (!user_args.check_required_flags(preprocess_required)){
return false;
}
// add default flag values if user did not specify values
if (user_args.args.count("--min-reads") == 0){
user_args.args.insert({"--min-reads", "2"});
}
if (user_args.args.count("-t") == 0){
user_args.args.insert({"-t", "3"});
}
if (user_args.args.count("--min-mapq") == 0){
user_args.args.insert({"--min-mapq", "10"});
}
if (!user_args.check_file("--graph", ".gfa")){
std::cout << "[preprocess::check_args][ERROR] could not open graph file: " << user_args.args["--graph"] << '\n';
return false;
}
if (!user_args.check_file("--reference", ".fa")){
std::cout << "[preprocess::check_args][ERROR] could not open reference file: " << user_args.args["--reference"] << '\n';
return false;
}
return true;
}
/* Identifies tumor-only unitigs from given .gfa file */
bool preprocess::filter_unitigs(ArgumentParser& user_args){
std::ifstream gfa_file(user_args.args["--graph"]);
std::ofstream out_tumor_utg_all(user_args.args["-o"] + "/intermediate_output/all_tumor_only_unitigs.txt");
std::ofstream out_tumor_utg_thresh(user_args.args["-o"] + "/intermediate_output/thresh_tumor_only_unitigs.txt");
std::ofstream out_tumor_fa(user_args.args["-o"] + "/intermediate_output/tumor_only_unitigs.fa");
// parse tumor sample IDs into list
std::vector<std::string> tumor_ids;
std::string s = user_args.args["--tumor-ids"];
std::string::const_iterator start = s.begin();
std::string::const_iterator end = s.end();
std::string::const_iterator next = std::find(start, end, ',');
while (next != end) {
tumor_ids.push_back(std::string(start, next));
start = next + 1;
next = std::find(start, end, ',');
}
tumor_ids.push_back(std::string(start, next));
int read_thresh {std::stoi(user_args.args["--min-reads"])};
char read_delim {user_args.args["--read-sep"][0]};
// ignore telomere sequences
std::string tel_seq_for {"TTAGGGTTAGGGTTAGGGTTAGGGTTAGGG"};
std::string tel_seq_rev {"CCCTAACCCTAACCCTAACCCTAACCCTAA"};
// variables for parsing .gfa file
std::string line_type, unitig, ignore, segment, read_id;
int num_tumor_reads{0};
int num_healthy_reads{0};
// double check we're starting with a segment line
gfa_file >> line_type;
if (line_type.c_str()[0] != 'S'){
std::cout << "[preprocess::filter_unitigs][ERROR] .gfa file must begin with S line\n";
return false;
}
gfa_file >> unitig >> segment;
gfa_file.ignore(std::numeric_limits<std::streamsize>::max(), '\n');
while(gfa_file >> line_type){
if (line_type.c_str()[0] == 'S'){
// end of the node, so reset for the next node
// first, write unitig info if this is a tumor-only node
if(num_tumor_reads >= 0 && num_healthy_reads == 0){
out_tumor_utg_all << unitig << '\n';
// only keep candidates above read threshold that do not contain telomere sequence
if (num_tumor_reads >= read_thresh && !(segment.find(tel_seq_for) != std::string::npos || segment.find(tel_seq_rev) != std::string::npos)){
out_tumor_utg_thresh << unitig << '\n';
out_tumor_fa << '>' << unitig << '\n' << segment << '\n';
}
}
gfa_file >> unitig >> segment;
num_tumor_reads = 0;
num_healthy_reads = 0;
}else if (line_type.c_str()[0] == 'A'){
gfa_file >> ignore >> ignore >> ignore >> read_id;
// check if this read comes from a non-tumor sample
if (std::find(std::begin(tumor_ids), std::end(tumor_ids), read_id.substr(0, read_id.find(read_delim))) != std::end(tumor_ids)){
num_tumor_reads++;
}else{
num_healthy_reads++;
}
}
gfa_file.ignore(std::numeric_limits<std::streamsize>::max(), '\n');
}
if(num_tumor_reads >= 0 && num_healthy_reads == 0){
out_tumor_utg_all << unitig << '\n';
if (num_tumor_reads >= read_thresh){
out_tumor_utg_thresh << unitig << '\n';
out_tumor_fa << '>' << unitig << '\n' << segment << '\n';
}
}
// close input and output files
gfa_file.close();
out_tumor_utg_all.close();
out_tumor_utg_thresh.close();
out_tumor_fa.close();
return true;
}
bool preprocess::align_unitigs(ArgumentParser& user_args){
std::string cmd;
struct stat buffer;
// check for minimap executable in colorSV directory first, then $PATH
if (stat((user_args.args["exe_path"] + "minimap2").c_str(), &buffer) == 0){
cmd = user_args.args["exe_path"] + "minimap2";
}else{
cmd = "minimap2";
}
// tumor-only unitig alignment to reference
cmd += " -cx lr:hq -t" + user_args.args["-t"] + " --ds " + user_args.args["--reference"] + " " + user_args.args["-o"] + "/intermediate_output/tumor_only_unitigs.fa > " + user_args.args["-o"] + "/intermediate_output/tumor_only_unitigs.paf";
system(cmd.c_str());
// filter to only keep alignments with minimum MAPQ score
cmd = "awk '$12 >= " + user_args.args["--min-mapq"] + "' " + user_args.args["-o"] + "/intermediate_output/tumor_only_unitigs.paf > " + user_args.args["-o"] + "/intermediate_output/tumor_only_unitigs_mapq_filtered.paf";
system(cmd.c_str());
return true;
}