genetics.cuh File Reference

Provides utilities for working with genetic data in various formats. More...

#include "BitString.cuh"
#include "nucleotide.hpp"
#include <filesystem>
#include <istream>
#include <string>
#include <vector>

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Classes
struct	genetics::GeneManager
	Manages efficient loading of multiple genetic sequences from a combined file. More...
struct	genetics::GeneManager::GeneInfo
	Structure to track information about a gene in the combined file. More...

Namespaces
namespace	genetics
	Contains utilities for working with genetic data and file formats.

Typedefs
typedef BitString< Nucleotide, 2 >	Gene
	A specialized BitString for representing genetic sequences.

Enumerations
enum class	genetics::FileType {   genetics::GBK , genetics::FNA , genetics::DNA , genetics::DNA_BIN ,   genetics::DNA_BIN_COMBINED , genetics::UNKNOWN }
	Enumerates the supported genetic file formats. More...

Functions
Gene	genetics::from_gbk (const std::string &filename)
	Loads a gene from a GenBank format file.
Gene	genetics::from_fna (const std::string &filename)
	Loads a gene from a FASTA nucleotide format file.
Gene	genetics::from_dna (const std::string &filename)
	Loads a gene from a plain text DNA format file.
Gene	genetics::from_file (const std::string &filename)
	Loads a gene from a file with automatic format detection.
Gene	genetics::from_file (const std::filesystem::path &path)
	Loads a gene from a file path with automatic format detection.
Gene	genetics::from_file (const std::filesystem::directory_entry &entry)
	Loads a gene from a directory entry with automatic format detection.
void	genetics::to_dna (const Gene &gene, const std::string &filename)
	Saves a gene to a plain text DNA format file.
std::vector< Gene >	genetics::from_directory (const std::string &dirname)
	Loads all genes from files in a directory with automatic format detection.
std::vector< Gene >	genetics::from_directory (const std::string &dirname, FileType type)
	Loads all genes from files of a specific format in a directory.
std::vector< std::string >	genetics::get_dna_strings_from_directory (const std::string &dirname)
	Extracts DNA strings from all supported files in a directory.
FileType	genetics::get_file_type (const std::string &filename)
	Determines the file type based on its filename extension.
FileType	genetics::get_file_type (const std::filesystem::path &path)
	Determines the file type based on its path's extension.
FileType	genetics::get_file_type (const std::filesystem::directory_entry &entry)
	Determines the file type based on a directory entry's path extension.
Gene	genetics::from_stream (std::istream &stream)
	Loads a gene from an input stream.
std::vector< std::filesystem::path >	genetics::get_virus_nucleotide_paths ()
	Gets paths to all virus nucleotide files in the virus directory.
void	genetics::combine_dna_bin_files (const std::string &dirname, const std::string &combined_filename)
	Combines multiple binary DNA files into a single combined file.

Variables
static const std::string	genetics::GENETIC_DIRECTORY = "genetic/"
	Path to the genetic data directory.
static const std::string	genetics::VIRUS_DIRECTORY = GENETIC_DIRECTORY + "virus/"
	Path to the virus genome data directory.
static const std::string	genetics::ABC_HUMI_DIRECTORY = GENETIC_DIRECTORY + "ABC-HuMi/"
	Path to the ABC-HuMi dataset directory.
static const std::string	genetics::DNA_EXTENSION = ".dna"
	File extension for plain text DNA files.
static const std::string	genetics::DNA_BIN_EXTENSION = ".dna.bin"
	File extension for binary DNA files.
static const std::string	genetics::DNA_BIN_COMBINED_EXTENSION = ".dna.bin.combined"
	File extension for combined binary DNA files.
static const std::string	genetics::DNA_BIN_SIZES_EXTENSION = ".dna.bin.sizes"
	File extension for binary DNA file size information.
static const std::string	genetics::GBK_EXTENSION = ".gbk"
	File extension for GenBank format files.
static const std::string	genetics::FNA_EXTENSION = ".fna"
	File extension for FASTA nucleotide format files.

Detailed Description

Provides utilities for working with genetic data in various formats.

This file defines types and functions for loading, saving, and manipulating genetic data from various file formats such as GBK, FNA, and DNA. It uses the BitString template specialized for nucleotides to efficiently represent genetic sequences.

See also

BitString.cuh

nucleotide.hpp

Definition in file genetics.cuh.

Typedef Documentation

Gene

Gene

A specialized BitString for representing genetic sequences.

Represents DNA sequences as bit strings with 2 bits per nucleotide, allowing for compact representation and efficient operations on genetic data.

Definition at line 28 of file genetics.cuh.