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code reformat
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Signed-off-by: Radu Muntean <[email protected]>
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@heracle
heracle committed Aug 10, 2021
1 parent f908467 commit 18c0fe0
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Showing 3 changed files with 91 additions and 88 deletions.
113 changes: 57 additions & 56 deletions metagraph/src/annotation/taxonomy/tax_classifier.cpp
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Original file line number Diff line number Diff line change
@@ -1,46 +1,29 @@
#include "tax_classifier.hpp"

#include <cmath>
#include <string>
#include <vector>

#include "annotation/representation/annotation_matrix/annotation_matrix.hpp"
#include "common/unix_tools.hpp"
#include "common/utils/string_utils.hpp"

#include "common/logger.hpp"

namespace mtg {
namespace annot {

using mtg::common::logger;

bool TaxonomyBase::assign_label_type(const std::string &sample_label) {
if (utils::starts_with(sample_label, "gi|")) {
// e.g. >gi|1070643132|ref|NC_031224.1| Arthrobacter phage Mudcat, complete genome
label_type = GEN_BANK;
return true;
} else if (utils::starts_with(utils::split_string(sample_label, ":")[1], "taxid|")) {
// e.g. >kraken:taxid|2016032|NC_047834.1 Alteromonas virus vB_AspP-H4/4, complete genome
label_type = TAXID;
return false;
}

logger->error("Can't determine the type of the given label {}. "
"Make sure the labels are in a recognized format.", sample_label);
exit(1);
}

bool TaxonomyBase::get_taxid_from_label(const std::string &label, TaxId *taxid) const {
if (label_type == TAXID) {
if (label_type_ == TAXID) {
*taxid = std::stoul(utils::split_string(label, "|")[1]);
return true;
} else if (TaxonomyBase::label_type == GEN_BANK) {
} else if (label_type_ == GEN_BANK) {
std::string acc_version = get_accession_version_from_label(label);
if (not accversion_to_taxid_map.count(acc_version)) {
auto it = accversion_to_taxid_map_.find(acc_version);
if (it == accversion_to_taxid_map_.end()) {
return false;
}
*taxid = accversion_to_taxid_map.at(acc_version);
*taxid = it->second;
return true;
}

Expand All @@ -49,9 +32,9 @@ bool TaxonomyBase::get_taxid_from_label(const std::string &label, TaxId *taxid)
}

std::string TaxonomyBase::get_accession_version_from_label(const std::string &label) const {
if (label_type == TAXID) {
if (label_type_ == TAXID) {
return utils::split_string(utils::split_string(label, "|")[2], " ")[0];
} else if (label_type == GEN_BANK) {
} else if (label_type_ == GEN_BANK) {
return utils::split_string(label, "|")[3];;
}

Expand All @@ -64,14 +47,16 @@ void TaxonomyBase::read_accversion_to_taxid_map(const std::string &filepath,
const graph::AnnotatedDBG *anno_matrix = NULL) {
std::ifstream f(filepath);
if (!f.good()) {
logger->error("Failed to open accession to taxid map table {}", filepath);
logger->error("Error: Failed to open accession to taxid map table {}. \n"
"In the cases when the taxid is not specified in the label string, "
"the acc_version to taxid lookup table filepath must be given as a flag.", filepath);
exit(1);
}

std::string line;
getline(f, line);
if (!utils::starts_with(line, "accession\taccession.version\ttaxid\t")) {
logger->error("The accession to taxid map table is not in the standard (*.accession2taxid) format {}",
logger->error("Error: The accession to taxid map table is not in the standard (*.accession2taxid) format {}",
filepath);
exit(1);
}
Expand All @@ -85,18 +70,18 @@ void TaxonomyBase::read_accversion_to_taxid_map(const std::string &filepath,

while (getline(f, line)) {
if (line == "") {
logger->error("The accession to taxid map table contains empty lines. "
logger->error("Error: The accession to taxid map table contains empty lines. "
"Please make sure that this file was not manually modified {}", filepath);
exit(1);
}
std::vector<std::string> parts = utils::split_string(line, "\t");
if (parts.size() <= 2) {
logger->error("The accession to taxid map table contains incomplete lines. "
logger->error("Error: The accession to taxid map table contains incomplete lines. "
"Please make sure that this file was not manually modified {}", filepath);
exit(1);
}
if (input_accessions.size() == 0 || input_accessions.count(parts[1])) {
accversion_to_taxid_map[parts[1]] = std::stoul(parts[2]);
accversion_to_taxid_map_[parts[1]] = std::stoul(parts[2]);
}
}
}
Expand All @@ -109,11 +94,29 @@ TaxonomyClsAnno::TaxonomyClsAnno(const graph::AnnotatedDBG &anno,
: TaxonomyBase(lca_coverage_rate, kmers_discovery_rate),
anno_matrix_(&anno) {
if (!std::filesystem::exists(tax_tree_filepath)) {
logger->error("Can't open taxonomic tree file {}", tax_tree_filepath);
logger->error("Error: Can't open taxonomic tree file {}", tax_tree_filepath);
exit(1);
}

bool require_accversion_to_taxid_map = assign_label_type(anno_matrix_->get_annotation().get_all_labels()[0]);
// Take one sample label and find the label type.
std::string sample_label = anno_matrix_->get_annotation().get_all_labels()[0];

// If true, require_accversion_to_taxid_map means that the taxid is not mentioned as part of the label. Thus, the program
// needs to parse an additional accession_version to taxid lookup file (optional argument: label_taxid_map_filepath).
bool require_accversion_to_taxid_map;
if (utils::starts_with(sample_label, "gi|")) {
// e.g. >gi|1070643132|ref|NC_031224.1| Arthrobacter phage Mudcat, complete genome
label_type_ = GEN_BANK;
require_accversion_to_taxid_map = true;
} else if (utils::starts_with(utils::split_string(sample_label, ":")[1], "taxid|")) {
// e.g. >kraken:taxid|2016032|NC_047834.1 Alteromonas virus vB_AspP-H4/4, complete genome
label_type_ = TAXID;
require_accversion_to_taxid_map = false;
} else {
logger->error("Error: Can't determine the type of the given label {}. "
"Make sure the labels are in a recognized format.", sample_label);
exit(1);
}

Timer timer;
if (require_accversion_to_taxid_map) {
Expand All @@ -131,7 +134,7 @@ TaxonomyClsAnno::TaxonomyClsAnno(const graph::AnnotatedDBG &anno,
timer.reset();
logger->trace("Calculating tree statistics...");
std::vector<TaxId> tree_linearization;
dfs_statistics(root_node, tree, &tree_linearization);
dfs_statistics(root_node_, tree, &tree_linearization);
logger->trace("Finished tree statistics calculation in {} sec.", timer.elapsed());

timer.reset();
Expand All @@ -143,39 +146,39 @@ TaxonomyClsAnno::TaxonomyClsAnno(const graph::AnnotatedDBG &anno,
void TaxonomyClsAnno::read_tree(const std::string &tax_tree_filepath, ChildrenList *tree) {
std::ifstream f(tax_tree_filepath);
if (!f.good()) {
logger->error("Failed to open Taxonomic Tree file {}", tax_tree_filepath);
logger->error("Error: Failed to open Taxonomic Tree file {}", tax_tree_filepath);
exit(1);
}

std::string line;
tsl::hopscotch_map<TaxId, TaxId> full_parents_list;
while (getline(f, line)) {
if (line == "") {
logger->error("The Taxonomic Tree file contains empty lines. "
logger->error("Error: The Taxonomic Tree file contains empty lines. "
"Please make sure that this file was not manually modified: {}",
tax_tree_filepath);
exit(1);
}
std::vector<std::string> parts = utils::split_string(line, "\t");
if (parts.size() <= 2) {
logger->error("The Taxonomic tree filepath contains incomplete lines. "
logger->error("Error: The Taxonomic tree filepath contains incomplete lines. "
"Please make sure that this file was not manually modified: {}",
tax_tree_filepath);
exit(1);
}
uint32_t act = std::stoul(parts[0]);
uint32_t parent = std::stoul(parts[2]);
full_parents_list[act] = parent;
node_parent[act] = parent;
node_parent_[act] = parent;
}

std::vector<TaxId> relevant_taxids;
// 'considered_relevant_taxids' is used to make sure that there are no duplications in 'relevant_taxids'.
tsl::hopscotch_set<TaxId> considered_relevant_taxids;

if (accversion_to_taxid_map.size()) {
if (accversion_to_taxid_map_.size()) {
// Store only the taxonomic nodes that exists in the annotation matrix.
for (const std::pair<std::string, TaxId> &pair : accversion_to_taxid_map) {
for (const std::pair<std::string, TaxId> &pair : accversion_to_taxid_map_) {
relevant_taxids.push_back(pair.second);
considered_relevant_taxids.insert(pair.second);
}
Expand Down Expand Up @@ -203,7 +206,7 @@ void TaxonomyClsAnno::read_tree(const std::string &tax_tree_filepath, ChildrenLi

// Check if the current taxid is the root.
if (taxid == full_parents_list[taxid]) {
root_node = taxid;
root_node_ = taxid;
}
}
if (num_taxid_failed) {
Expand All @@ -213,7 +216,7 @@ void TaxonomyClsAnno::read_tree(const std::string &tax_tree_filepath, ChildrenLi

// Construct the output tree.
for (const TaxId &taxid : relevant_taxids) {
if (taxid == root_node) {
if (taxid == root_node_) {
continue;
}
(*tree)[full_parents_list[taxid]].push_back(taxid);
Expand All @@ -223,7 +226,7 @@ void TaxonomyClsAnno::read_tree(const std::string &tax_tree_filepath, ChildrenLi
void TaxonomyClsAnno::dfs_statistics(const TaxId node,
const ChildrenList &tree,
std::vector<TaxId> *tree_linearization) {
node_to_linearization_idx[node] = tree_linearization->size();
node_to_linearization_idx_[node] = tree_linearization->size();
tree_linearization->push_back(node);
uint32_t depth = 0;

Expand All @@ -232,25 +235,25 @@ void TaxonomyClsAnno::dfs_statistics(const TaxId node,
for (const TaxId &child : it->second) {
dfs_statistics(child, tree, tree_linearization);
tree_linearization->push_back(node);
if (node_depth[child] > depth) {
depth = node_depth[child];
if (node_depth_[child] > depth) {
depth = node_depth_[child];
}
}
}
node_depth[node] = depth + 1;
node_depth_[node] = depth + 1;
}

void TaxonomyClsAnno::rmq_preprocessing(const std::vector<TaxId> &tree_linearization) {
uint32_t num_rmq_rows = log2(tree_linearization.size()) + 1;
uint32_t num_rmq_rows = sdsl::bits::hi(tree_linearization.size()) + 1;

rmq_data.resize(num_rmq_rows);
rmq_data_.resize(num_rmq_rows);
for (uint32_t i = 0; i < num_rmq_rows; ++i) {
rmq_data[i].resize(tree_linearization.size());
rmq_data_[i].resize(tree_linearization.size());
}

// Copy tree_linearization to rmq[0].
for (uint32_t i = 0; i < tree_linearization.size(); ++i) {
rmq_data[0][i] = tree_linearization[i];
rmq_data_[0][i] = tree_linearization[i];
}

// Delta represents the size of the RMQ's sliding window (always a power of 2).
Expand All @@ -262,27 +265,25 @@ void TaxonomyClsAnno::rmq_preprocessing(const std::vector<TaxId> &tree_lineariza
// According to 'this->dfs_statistics()':
// node_depth[leaf] = 1 and node_depth[root] = maximum distance to a leaf.

if (node_depth[rmq_data[row - 1][i]] >
node_depth[rmq_data[row - 1][i + delta]]) {
rmq_data[row][i] = rmq_data[row - 1][i];
if (node_depth_[rmq_data_[row - 1][i]] >
node_depth_[rmq_data_[row - 1][i + delta]]) {
rmq_data_[row][i] = rmq_data_[row - 1][i];
} else {
rmq_data[row][i] = rmq_data[row - 1][i + delta];
rmq_data_[row][i] = rmq_data_[row - 1][i + delta];
}
}
delta *= 2;
}
}

std::vector<TaxId> TaxonomyClsAnno::get_lca_taxids_for_seq(const std::string_view &sequence, bool reversed) const {
cerr << "Assign class not implemented reversed = " << reversed << "\n";
throw std::runtime_error("get_lca_taxids_for_seq TaxonomyClsAnno not implemented. Received seq size"
+ to_string(sequence.size()));
+ to_string(sequence.size()) + to_string(reversed));
}

std::vector<TaxId> TaxonomyClsImportDB::get_lca_taxids_for_seq(const std::string_view &sequence, bool reversed) const {
cerr << "Assign class not implemented reversed = " << reversed << "\n";
throw std::runtime_error("get_lca_taxids_for_seq TaxonomyClsImportDB not implemented. Received seq size"
+ to_string(sequence.size()));
+ to_string(sequence.size()) + to_string(reversed));
}

TaxId TaxonomyClsAnno::find_lca(const std::vector<TaxId> &taxids) const {
Expand Down
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