gesel Namespace Reference

Validate Gesel database and gene files. More...

Functions
void	validate_database (const std::string &prefix, uint64_t num_genes)
uint64_t	validate_genes (const std::string &prefix, const std::vector< std::string > &types)
uint64_t	validate_genes (const std::string &prefix)

Detailed Description

Validate Gesel database and gene files.

Function Documentation

validate_database()

void gesel::validate_database ( const std::string & prefix, uint64_t num_genes )

inline

Validate Gesel database files for a particular species. This checks all files for validity and consistency except for the gene mapping files (which are validated by validate_genes()). Any invalid formatting or inconsistency between files will result in an error.

Parameters

prefix	Prefix for the Gesel database files. This should be of the form <DIRECTORY>/<SPECIES>_, where <SPECIES> is an NCBI taxonomy ID.
num_genes	Total number of genes for this species.

validate_genes() [1/2]

uint64_t gesel::validate_genes ( const std::string & prefix )

inline

Overload for validate_genes(). This will scan the directory for all files starting with prefix and ending with ".tsv.gz".

Parameters

prefix

Prefix for the Gesel gene files. This should be of the form <DIRECTORY>/<SPECIES>_, where <SPECIES> is an NCBI taxonomy ID.

Returns

Number of genes.

validate_genes() [2/2]

uint64_t gesel::validate_genes ( const std::string & prefix, const std::vector< std::string > & types )

inline

Validate Gesel gene mapping files for a particular species. Any invalid formatting or inconsistency between files will result in an error.

Parameters

prefix	Prefix for the Gesel gene mapping files. This should be of the form <DIRECTORY>/<SPECIES>_, where <SPECIES> is an NCBI taxonomy ID.
types	Vector of gene name types, e.g., "ensembl", "symbol". This should contain at least one value.

Returns

Number of genes.