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consult_classify.cpp
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consult_classify.cpp
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#include <chrono>
#include <dirent.h>
#include <fstream>
#include <getopt.h>
#include <iostream>
#include <math.h>
#include <numeric>
#include <sstream>
#include <string.h> // for strcmp, strlen
#include <string>
#include <sys/stat.h>
#include <sys/types.h>
#include <tuple>
#include <unordered_map>
#include <unordered_set>
#include <vector>
using namespace std;
#define VERSION "v0.4.0"
#define PRINT_VERSION printf("CONSULT-II version: " VERSION "\n");
#define THREAD_COUNT_OPT 'T'
#define TAXONOMY_LOOKUP_PATH_OPT 'A'
#define KMER_LENGTH 32
namespace TaxonomicInfo {
enum Kingdoms { BACTERIA = 2, ARCHAEA = 2157 };
static const Kingdoms AllKingdoms[] = {BACTERIA, ARCHAEA};
} // namespace TaxonomicInfo
struct kmer_match {
uint16_t dist;
float vote;
uint64_t taxID;
};
struct read_info {
bool isRC;
string readID;
tuple<uint64_t, float, float> pred_taxID_info;
vector<kmer_match> match_vector;
};
vector<string> list_dir(const char *path) {
vector<string> userString;
struct dirent *entry;
DIR *dir = opendir(path);
while ((entry = readdir(dir)) != NULL) {
if ((strcmp(entry->d_name, "..") != 0) && (strcmp(entry->d_name, ".") != 0)) {
userString.push_back(string(path) + "/" + entry->d_name);
}
}
closedir(dir);
return (userString);
}
void read_taxonomy_lookup(string filepath, unordered_map<uint64_t, vector<uint64_t>> &taxonomy_lookup) {
ifstream ftable;
ftable.open(filepath);
if (!ftable) {
cout << "Cannot open file for taxonomic lookup table." << endl;
exit(1);
}
for (string line; getline(ftable, line);) {
istringstream iss(line);
string taxIDstr;
getline(iss, taxIDstr, ' ');
uint64_t taxID = stoi(taxIDstr);
vector<uint64_t> lineage;
string next_taxIDstr;
while (getline(iss, next_taxIDstr, ',')) {
lineage.push_back(stoi(next_taxIDstr));
}
taxonomy_lookup.insert({taxID, lineage});
}
}
void read_matches(string filepath, vector<read_info> &all_read_info) {
ifstream infile(filepath);
string line;
string readID;
uint64_t line_counter = 0;
uint16_t k = KMER_LENGTH;
while (getline(infile, line)) {
istringstream iss(line);
if ((line_counter % 3) == 0)
iss >> readID;
else {
bool isRC;
string tmp;
if ((line_counter % 3) == 1) {
isRC = false;
iss >> tmp;
} else {
isRC = true;
iss >> tmp;
}
string match_str;
vector<kmer_match> match_vector;
while (iss >> match_str) {
stringstream ss(match_str);
string taxID_str;
string dist_str;
getline(ss, taxID_str, ':');
getline(ss, dist_str, ':');
kmer_match curr_match;
curr_match.dist = stoi(dist_str);
curr_match.taxID = stoi(taxID_str);
curr_match.vote = pow((1.0 - curr_match.dist / (float)k), k);
match_vector.push_back(curr_match);
}
read_info curr_read;
curr_read.readID = readID;
curr_read.isRC = isRC;
curr_read.match_vector = match_vector;
all_read_info.push_back(curr_read);
}
line_counter++;
}
}
unordered_map<uint64_t, float> get_rank_votes(kmer_match amatch,
unordered_map<uint64_t, vector<uint64_t>> &taxonomy_lookup) {
uint16_t k = KMER_LENGTH;
unordered_map<uint64_t, float> match_votes;
for (uint64_t a_taxID : taxonomy_lookup[amatch.taxID]) {
if ((a_taxID > 0) && (amatch.taxID > 0))
match_votes[a_taxID] = amatch.vote;
}
return match_votes;
}
void aggregate_votes(unordered_map<uint64_t, vector<uint64_t>> taxonomy_lookup, vector<read_info> &all_read_info,
int thread_count) {
#pragma omp parallel for schedule(dynamic, 1) num_threads(thread_count) shared(taxonomy_lookup, all_read_info)
for (int ix = 0; ix < all_read_info.size(); ++ix) {
read_info &curr_read = all_read_info[ix];
uint64_t rootID = 1;
pair<uint64_t, float> identity(rootID, 0.0);
pair<uint64_t, float> maxID(0, 0.0);
float max_vote = 0.0;
uint8_t max_depth = 0;
if (curr_read.match_vector.size() > 0) {
unordered_map<uint64_t, vector<float>> vote_collector;
unordered_map<uint64_t, float> final_votes;
unordered_set<uint64_t> all_taxIDs;
unordered_map<uint16_t, unordered_set<uint64_t>> taxIDs_by_rank;
for (auto &curr_match : curr_read.match_vector) {
unordered_map<uint64_t, float> match_votes;
#pragma omp critical
{ match_votes = get_rank_votes(curr_match, taxonomy_lookup); }
for (auto &vote : match_votes) {
vote_collector[vote.first].push_back(vote.second);
all_taxIDs.insert(vote.first);
#pragma omp critical
{
taxIDs_by_rank[(int)taxonomy_lookup[vote.first].size()].insert(vote.first);
if (max_depth < taxonomy_lookup[vote.first].size())
max_depth = taxonomy_lookup[vote.first].size();
}
}
}
vector<uint64_t> taxIDs_vec(all_taxIDs.begin(), all_taxIDs.end());
for (uint64_t taxID : taxIDs_vec) {
final_votes[taxID] = accumulate(vote_collector[taxID].begin(), vote_collector[taxID].end(), 0.0);
}
for (const auto &taxon : TaxonomicInfo::AllKingdoms) {
max_vote += final_votes[static_cast<int>(taxon)];
}
float th_vote = 0.5 * max_vote;
for (uint16_t lvl = max_depth; lvl >= 1; --lvl) {
vector<uint64_t> taxIDs_vec_lvl(taxIDs_by_rank[lvl].begin(), taxIDs_by_rank[lvl].end());
for (auto &taxID : taxIDs_vec_lvl) {
if (final_votes[taxID] > th_vote) {
maxID.first = taxID;
maxID.second = final_votes[taxID];
break;
}
}
if (maxID.second > th_vote)
break;
}
}
get<0>(curr_read.pred_taxID_info) = maxID.first;
get<1>(curr_read.pred_taxID_info) = maxID.second;
get<2>(curr_read.pred_taxID_info) = max_vote;
}
}
void write_classifications_to_file(string filepath, vector<read_info> all_read_info) {
ofstream outfile(filepath);
string read_form;
int num_reads = all_read_info.size() / 2;
for (int ix = 0; ix < num_reads; ++ix) {
float rc_vote = get<1>(all_read_info[2 * ix + 1].pred_taxID_info);
float os_vote = get<1>(all_read_info[2 * ix].pred_taxID_info);
read_info curr_read;
if (rc_vote > os_vote) {
read_form = "rc";
curr_read = all_read_info[2 * ix + 1];
} else {
read_form = "--";
curr_read = all_read_info[2 * ix];
}
outfile << curr_read.readID << "\t" << read_form << "\t" << to_string(get<0>(curr_read.pred_taxID_info)) << "\t"
<< to_string(get<1>(curr_read.pred_taxID_info)) << "\t" << to_string(get<2>(curr_read.pred_taxID_info))
<< endl;
}
outfile.close();
}
int main(int argc, char *argv[]) {
PRINT_VERSION
uint64_t thread_count = 1;
char *input_path = NULL;
string taxonomy_lookup_path;
string output_predictions_dir = ".";
int cf_tmp;
opterr = 0;
while (1) {
static struct option long_options[] = {
{"input-matches-path", 1, 0, 'i'},
{"output-predictions-dir", 1, 0, 'o'},
{"taxonomy-lookup-path", 1, 0, TAXONOMY_LOOKUP_PATH_OPT},
{"thread-count", 1, 0, THREAD_COUNT_OPT},
{0, 0, 0, 0},
};
int option_index = 0;
cf_tmp = getopt_long(argc, argv, "i:o:", long_options, &option_index);
if ((optarg != NULL) && (*optarg == '-')) {
cf_tmp = ':';
}
if (cf_tmp == -1)
break;
else if (cf_tmp == TAXONOMY_LOOKUP_PATH_OPT)
taxonomy_lookup_path = optarg;
else if (cf_tmp == THREAD_COUNT_OPT)
thread_count = atoi(optarg); // Default is 1.
else {
switch (cf_tmp) {
case 'i':
input_path = optarg;
break;
case 'o':
output_predictions_dir = optarg;
break;
case '?':
if (optopt == 'i')
fprintf(stderr, "Option -%c requires an argument.\n", optopt);
else if (optopt == 'q')
fprintf(stderr, "Option -%c requires an argument.\n", optopt);
else if (isprint(optopt))
fprintf(stderr, "Unknown option '-%c'.\n", optopt);
else
fprintf(stderr, "Unknown option '%s'.\n", argv[optind - 1]);
return 1;
default:
abort();
}
}
}
cout << "Number of threads is " << thread_count << "." << endl;
struct stat s_input_path;
vector<string> match_info_path_list;
if (stat(input_path, &s_input_path) == 0) {
if (s_input_path.st_mode & S_IFDIR) {
match_info_path_list = list_dir(input_path);
} else if (s_input_path.st_mode & S_IFREG) {
match_info_path_list.push_back(input_path);
} else {
cout << "Filetype in the given query path is not recognized." << endl;
exit(1);
}
} else {
cout << "Given query path is not valid!" << endl;
exit(1);
}
int total_readTime = 0;
int total_classificationTime = 0;
int total_numberOfReads = 0;
chrono::steady_clock::time_point t1;
chrono::steady_clock::time_point t2;
for (string input_path : match_info_path_list) {
string query_name = input_path.substr(input_path.find_last_of("/") + 1);
query_name = query_name.substr(0, query_name.find_last_of("."));
query_name = query_name.substr(query_name.find_first_of("_") + 1);
string output_path = output_predictions_dir + "/" + "classification_" + query_name;
cout << "Now processing: " << query_name << endl;
unordered_map<uint64_t, vector<uint64_t>> taxonomy_lookup;
read_taxonomy_lookup(taxonomy_lookup_path, taxonomy_lookup);
vector<read_info> all_read_info;
t1 = chrono::steady_clock::now();
read_matches(input_path, all_read_info);
t2 = chrono::steady_clock::now();
total_readTime += chrono::duration_cast<chrono::milliseconds>(t2 - t1).count();
total_numberOfReads += all_read_info.size();
t1 = chrono::steady_clock::now();
aggregate_votes(taxonomy_lookup, all_read_info, thread_count);
t2 = chrono::steady_clock::now();
total_classificationTime += chrono::duration_cast<chrono::milliseconds>(t2 - t1).count();
write_classifications_to_file(output_path, all_read_info);
}
cout << "Time past (read_matches) = " << total_readTime << "[ms]" << endl;
cout << "Time past (aggregate_votes) = " << total_classificationTime << "[ms]" << endl;
cout << "Total number of reads processed: " << total_numberOfReads / 2 << endl;
}