Provides global variables used all over the project. More...

Functions
def	GetConfig ()
	Get the global configuration object. More...

Variables
int	PY_VER = 10*sys.version_info[0] + sys.version_info[1];
	This interpreter's version as a two digit number, major and minor release. More...

string	CSV_SEP = "\t";
	Default separator for tabular-like (ie. More...

string	CELL_NO_DATA = "--";
	Indicator for empty cell when writing out tables. More...

string	VCF_NO_DATA = "."
	Default empty cell value of the VCF format, as defined by the 1000 Genomes project. More...

string	GATK_NO_DATA = "./."
	Empty cell value put by the GATK tools. More...

string	DEFAULT_DATA_VERSION = "v-00";
	Default section name, also used for requesting default path configuration. More...

string	ENSEMBL_HSGENE_DB = "hsgene-0";
	Ensembl protein database, used by multiple conversion modules. More...

	DI_ROOT = os.path.normpath(os.path.join(_dirNm, "..", "..", ".."));
	Top level directory for the D-integrator project. More...

	DI_PY_ROOT = os.path.normpath(os.path.join(DI_ROOT, "src", "python"));
	Directory for python sources. More...

	idx = sys.argv.index("--config")

string	errMsg = "Cannot open configuration file ``{0}''.\n".format(_configFN);

	DI_VERSION = _Config.get("DEFAULT", "di.version");
	The Data Integrator software and data version, an overall tag. More...

string	CFG_HS_GENOME_BUILD_VERSION = "ensembl.hs.genome.build.version";
	Current Ensembl genome build version token for config file. More...

string	TAXID_HUMAN = "9606"

tuple	GO_NAMESPACES
	Gene ontology namespace abbreviations, their long names, and as they appear in GO annotation corpora. More...

int	GO_MF_IDX = 0;
	Index into GO_NAMESPACES for molecular function. More...

int	GO_BP_IDX = 1;
	Index into GO_NAMESPACES for biological process. More...

int	GO_CC_IDX = 2;
	Index into GO_NAMESPACES for cellular component. More...

int	GO_NS2L_IDX = 0;
	Gene ontology two letter abbreviation index into GO_NAMESPACES. More...

int	GO_NSFULL_IDX = 1;
	Gene ontology full namespace text index into GO_NAMESPACES. More...

int	GO_NS1L_IDX = 2;
	Gene ontology one letter abbreviation index into GO_NAMESPACES. More...

string	OP_AND = "AND"

string	OP_OR = "OR"

Detailed Description

Provides global variables used all over the project.

Author: Chris X. Weichenberger

Date: 2012-02-06

Copyright: See LICENSE file.

Function Documentation

◆ GetConfig()

def common.Globals.GetConfig ( )

Get the global configuration object.

Variable Documentation

◆ CELL_NO_DATA

string common.Globals.CELL_NO_DATA = "--";

Indicator for empty cell when writing out tables.

Other possibility is the empty string "".

◆ CFG_HS_GENOME_BUILD_VERSION

string common.Globals.CFG_HS_GENOME_BUILD_VERSION = "ensembl.hs.genome.build.version";

Current Ensembl genome build version token for config file.

It's value is config file section dependent and therefore even different genome builds can be used within the same release!!

◆ CSV_SEP

string common.Globals.CSV_SEP = "\t";

Default separator for tabular-like (ie.

csv) files.

◆ DEFAULT_DATA_VERSION

string common.Globals.DEFAULT_DATA_VERSION = "v-00";

Default section name, also used for requesting default path configuration.

◆ DI_PY_ROOT

common.Globals.DI_PY_ROOT = os.path.normpath(os.path.join(DI_ROOT, "src", "python"));

Directory for python sources.

◆ DI_ROOT

common.Globals.DI_ROOT = os.path.normpath(os.path.join(_dirNm, "..", "..", ".."));

Top level directory for the D-integrator project.

◆ DI_VERSION

common.Globals.DI_VERSION = _Config.get("DEFAULT", "di.version");

The Data Integrator software and data version, an overall tag.

◆ ENSEMBL_HSGENE_DB

string common.Globals.ENSEMBL_HSGENE_DB = "hsgene-0";

Ensembl protein database, used by multiple conversion modules.

◆ errMsg

string common.Globals.errMsg = "Cannot open configuration file ``{0}''.\n".format(_configFN);

◆ GATK_NO_DATA

string common.Globals.GATK_NO_DATA = "./."

Empty cell value put by the GATK tools.

◆ GO_BP_IDX

int common.Globals.GO_BP_IDX = 1;

Index into GO_NAMESPACES for biological process.

◆ GO_CC_IDX

int common.Globals.GO_CC_IDX = 2;

Index into GO_NAMESPACES for cellular component.

◆ GO_MF_IDX

int common.Globals.GO_MF_IDX = 0;

Index into GO_NAMESPACES for molecular function.

◆ GO_NAMESPACES

tuple common.Globals.GO_NAMESPACES

Initial value:

 =  ( ("MF", "molecular_function", "F", ),
                   ("BP", "biological_process", "P"),
                   ("CC", "cellular_component", "C") );

Gene ontology namespace abbreviations, their long names, and as they appear in GO annotation corpora.

◆ GO_NS1L_IDX

int common.Globals.GO_NS1L_IDX = 2;

Gene ontology one letter abbreviation index into GO_NAMESPACES.

◆ GO_NS2L_IDX

int common.Globals.GO_NS2L_IDX = 0;

Gene ontology two letter abbreviation index into GO_NAMESPACES.

◆ GO_NSFULL_IDX

int common.Globals.GO_NSFULL_IDX = 1;

Gene ontology full namespace text index into GO_NAMESPACES.

◆ idx

common.Globals.idx = sys.argv.index("--config")

◆ OP_AND

string common.Globals.OP_AND = "AND"

◆ OP_OR

string common.Globals.OP_OR = "OR"

◆ PY_VER

int common.Globals.PY_VER = 10*sys.version_info[0] + sys.version_info[1];

This interpreter's version as a two digit number, major and minor release.

◆ TAXID_HUMAN

string common.Globals.TAXID_HUMAN = "9606"

◆ VCF_NO_DATA

string common.Globals.VCF_NO_DATA = "."

Default empty cell value of the VCF format, as defined by the 1000 Genomes project.

Functions

Variables