A toolkit for working with phylogenetic data.
v0.20.0
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ncbi.hpp File Reference
#include "genesis/taxonomy/taxon.hpp"
#include "genesis/taxonomy/taxonomy.hpp"
#include "genesis/utils/formats/csv/reader.hpp"
#include <string>
#include <unordered_map>

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Classes

struct  NcbiName
 
struct  NcbiNode
 

Namespaces

 genesis
 Container namespace for all symbols of genesis in order to keep them separate when used as a library.
 
 genesis::taxonomy
 

Typedefs

using NcbiNameLookup = std::unordered_map< std::string, NcbiName >
 
using NcbiNodeLookup = std::unordered_map< std::string, NcbiNode >
 

Functions

NcbiNameLookup convert_ncbi_name_table (utils::CsvReader::Table const &name_table, size_t tax_id_pos, size_t name_pos, size_t name_class_pos, std::string name_class_filter)
 
NcbiNodeLookup convert_ncbi_node_table (utils::CsvReader::Table const &node_table, size_t tax_id_pos, size_t parent_tax_id_pos, size_t rank_pos)
 
Taxonomy convert_ncbi_tables (NcbiNodeLookup const &nodes, NcbiNameLookup const &names)
 
Taxonomy read_ncbi_taxonomy (std::string const &node_file, std::string const &name_file)