Provides full path (file) names to modules, handling data versions for a release. More...

Classes
class	CPaths
	Handling of versioned data files for all modules. More...

Variables
string	PARAM_ENSEMBL_HS_GENOME_BUILD_VER = "ensembl.hs.genome.build.version";

string	PARAM_ENSEMBL_VER = "ensembl.version";

string	PTH_EBI_BIOMART_HS_ENSG2ENTREZ = "ebi.biomart.hs.e2entrez";

string	PTH_EBI_BIOMART_HS_ENSG2HGNC = "ebi.biomart.hs.e2hgnc";

string	PTH_HGNC_BIOMART_HS_HGNC2ALIASES = "hgnc.biomart.hgnc2aliases";

string	PTH_EBI_BIOMART_HS_ENSG2ENST = "ebi.biomart.hs.e2enst";

string	PTH_EBI_BIOMART_HS_ENST2CCDS = "ebi.biomart.hs.enst2ccds";

string	PTH_EBI_BIOMART_HS_ENST2ENSP = "ebi.biomart.hs.enst2ensp";

string	PTH_EBI_BIOMART_HS_ENSG2UNIPROTSWISSPROT = "ebi.biomart.hs.e2uniprotswissprot";

string	PTH_EBI_BIOMART_HS_ENSG2UNIPROTTREMBL = "ebi.biomart.hs.e2uniprottrembl";

string	PTH_EBI_BIOMART_DM_FBGN2CGID = "ebi.biomart.dm.fbgn2cgid";

string	PTH_UNIPROT_HS_ACCESSION2ENTRYNAME = "uniprot.hs.accession2entryname";

string	PTH_EBI_BIOMART_HS_DM_ORTHOLOGY = "ebi.biomart.hs.dm.orthologs";

string	PTH_EBI_BIOMART_HS_MM_ORTHOLOGY = "ebi.biomart.hs.mm.orthologs";

string	PTH_EBI_BIOMART_HS_CE_ORTHOLOGY = "ebi.biomart.hs.ce.orthologs";

string	PTH_EBI_BIOMART_HS_ENSG = "ebi.biomart.hs.ensg";

string	PTH_VDRC_R57_DM_TRFID2CGID = "vdrc.r57.dm.trfid2cgid";

string	PTH_VDRC_R538_DM_TRFID2CGID = "vdrc.r538.dm.trfid2cgid";

string	PTH_VDRC_R601_DM_TRFID2CGID = "vdrc.r601.dm.trfid2cgid";

string	PTH_EURAC_INTERNAL_GLOBAL_LD_1000G = "eurac.internal.global.ld.1000G";

	PARAM_EURAC_INTERNAL_GLOBAL_LD_1000G_VER = \

string	PTH_GNF_HS_GENEATLAS = "gnf.hs.geneatlas";

string	PARAM_GNF_HS_GENEATLAS_VER = "gnf.hs.geneatlas.version";

string	PTH_MISC_PHARMADME_COREMARKERS = "misc.pharmaadme.coremarkers";

string	PARAM_MISC_PHARMADME_COREMARKERS_VER = "misc.pharmaadme.coremarkers.version";

string	PARAM_CBM_DB_HGMD_USER = "cbm.db.hgmd.user";

string	PARAM_CBM_DB_HGMD_PASSWD = "cbm.db.hgmd.passwd";

string	PARAM_CBM_DB_HGMD_HOST = "cbm.db.hgmd.host";

string	PARAM_CBM_DB_HGMD_SCHEMA = "cbm.db.hgmd.schema";

string	PARAM_CBM_DB_HGMD_VER = "cbm.db.hgmd.version";

string	PARAM_CBM_DB_GO_USER = "cbm.db.go.user";

string	PARAM_CBM_DB_GO_PASSWD = "cbm.db.go.passwd";

string	PARAM_CBM_DB_GO_HOST = "cbm.db.go.host";

string	PARAM_CBM_DB_GO_SCHEMA = "cbm.db.go.schema";

string	PARAM_CBM_DB_GO_PORT = "cbm.db.go.port";

string	PARAM_CBM_DB_GO_VER = "cbm.db.go.version";

string	PTH_NCBI_CLINVAR_DAT = "ncbi.clinvar.dat";

string	PTH_INTERACTION_MITAB = "interactions.mitab"

string	PARAM_INTERACTIONS_PRIMARYIDS = "interactions.primaryids"

string	PARAM_INTERACTIONS_VER = "interactions.version";

string	PARAM_INTERACTIONS_DB = "interactions.db";

string	PTH_WISHART_DRUGBANK_XSD = "wishart.drugbank.xsd";

string	PTH_WISHART_DRUGBANK_XML = "wishart.drugbank.xml";

string	PARAM_WISHART_DRUGBANK_VER = "wishart.drugbank.version";

string	PTH_REACTOME_BIOPAX = "reactome.biopax"

string	PARAM_REACTOME_VER = "reactome.version";

string	PTH_GO_GRAPH_BP_POPULATED = "go.graph.bp.populated";

string	PTH_GO_GRAPH_MF_POPULATED = "go.graph.mf.populated";

string	PTH_GO_GRAPH_CC_POPULATED = "go.graph.cc.populated";

string	PTH_GO_GOA_HUMAN = "go.goa.human";

string	PARAM_CBM_DB_MITAB_USER = "cbm.db.mitab.user";

string	PARAM_CBM_DB_MITAB_PASSWD = "cbm.db.mitab.passwd";

string	PARAM_CBM_DB_MITAB_HOST = "cbm.db.mitab.host";

string	PARAM_CBM_DB_MITAB_PORT = "cbm.db.mitab.port";

string	PARAM_CBM_DB_MITAB_SCHEMA = "cbm.db.mitab.schema";

string	PARAM_CBM_DB_MITAB_SCHEMA_MAPPED = "cbm.db.mitab.schema.mapped";

Detailed Description

Provides full path (file) names to modules, handling data versions for a release.

Author: Chris X. Weichenberger; Hagen Blankenburg

Date: 2012-02-15

Copyright: See LICENSE file.

Provides full path (file) names to modules, handling data versions for a release.

Author : Chris Weichenberger Created : 2012-02-15 Modifications: 2012-03-23 (CW) Removed absolute paths in config file. Absolute path is assembled here now. 2012-08-30 (CW) Fit for re-use in other projects. 2012-11-08 (CW) 1000 Genomes LD path. 2013-03-12 (HB) CBM DB paths 2013-12-20 (AP) Removed possible-orthologs paths.

Variable Documentation

◆ PARAM_CBM_DB_GO_HOST

string common.Paths.PARAM_CBM_DB_GO_HOST = "cbm.db.go.host";

◆ PARAM_CBM_DB_GO_PASSWD

string common.Paths.PARAM_CBM_DB_GO_PASSWD = "cbm.db.go.passwd";

◆ PARAM_CBM_DB_GO_PORT

string common.Paths.PARAM_CBM_DB_GO_PORT = "cbm.db.go.port";

◆ PARAM_CBM_DB_GO_SCHEMA

string common.Paths.PARAM_CBM_DB_GO_SCHEMA = "cbm.db.go.schema";

◆ PARAM_CBM_DB_GO_USER

string common.Paths.PARAM_CBM_DB_GO_USER = "cbm.db.go.user";

◆ PARAM_CBM_DB_GO_VER

string common.Paths.PARAM_CBM_DB_GO_VER = "cbm.db.go.version";

◆ PARAM_CBM_DB_HGMD_HOST

string common.Paths.PARAM_CBM_DB_HGMD_HOST = "cbm.db.hgmd.host";

◆ PARAM_CBM_DB_HGMD_PASSWD

string common.Paths.PARAM_CBM_DB_HGMD_PASSWD = "cbm.db.hgmd.passwd";

◆ PARAM_CBM_DB_HGMD_SCHEMA

string common.Paths.PARAM_CBM_DB_HGMD_SCHEMA = "cbm.db.hgmd.schema";

◆ PARAM_CBM_DB_HGMD_USER

string common.Paths.PARAM_CBM_DB_HGMD_USER = "cbm.db.hgmd.user";

◆ PARAM_CBM_DB_HGMD_VER

string common.Paths.PARAM_CBM_DB_HGMD_VER = "cbm.db.hgmd.version";

◆ PARAM_CBM_DB_MITAB_HOST

string common.Paths.PARAM_CBM_DB_MITAB_HOST = "cbm.db.mitab.host";

◆ PARAM_CBM_DB_MITAB_PASSWD

string common.Paths.PARAM_CBM_DB_MITAB_PASSWD = "cbm.db.mitab.passwd";

◆ PARAM_CBM_DB_MITAB_PORT

string common.Paths.PARAM_CBM_DB_MITAB_PORT = "cbm.db.mitab.port";

◆ PARAM_CBM_DB_MITAB_SCHEMA

string common.Paths.PARAM_CBM_DB_MITAB_SCHEMA = "cbm.db.mitab.schema";

◆ PARAM_CBM_DB_MITAB_SCHEMA_MAPPED

string common.Paths.PARAM_CBM_DB_MITAB_SCHEMA_MAPPED = "cbm.db.mitab.schema.mapped";

◆ PARAM_CBM_DB_MITAB_USER

string common.Paths.PARAM_CBM_DB_MITAB_USER = "cbm.db.mitab.user";

◆ PARAM_ENSEMBL_HS_GENOME_BUILD_VER

string common.Paths.PARAM_ENSEMBL_HS_GENOME_BUILD_VER = "ensembl.hs.genome.build.version";

◆ PARAM_ENSEMBL_VER

string common.Paths.PARAM_ENSEMBL_VER = "ensembl.version";

◆ PARAM_EURAC_INTERNAL_GLOBAL_LD_1000G_VER

common.Paths.PARAM_EURAC_INTERNAL_GLOBAL_LD_1000G_VER = \

◆ PARAM_GNF_HS_GENEATLAS_VER

string common.Paths.PARAM_GNF_HS_GENEATLAS_VER = "gnf.hs.geneatlas.version";

◆ PARAM_INTERACTIONS_DB

string common.Paths.PARAM_INTERACTIONS_DB = "interactions.db";

◆ PARAM_INTERACTIONS_PRIMARYIDS

string common.Paths.PARAM_INTERACTIONS_PRIMARYIDS = "interactions.primaryids"

◆ PARAM_INTERACTIONS_VER

string common.Paths.PARAM_INTERACTIONS_VER = "interactions.version";

◆ PARAM_MISC_PHARMADME_COREMARKERS_VER

string common.Paths.PARAM_MISC_PHARMADME_COREMARKERS_VER = "misc.pharmaadme.coremarkers.version";

◆ PARAM_REACTOME_VER

string common.Paths.PARAM_REACTOME_VER = "reactome.version";

◆ PARAM_WISHART_DRUGBANK_VER

string common.Paths.PARAM_WISHART_DRUGBANK_VER = "wishart.drugbank.version";

◆ PTH_EBI_BIOMART_DM_FBGN2CGID

string common.Paths.PTH_EBI_BIOMART_DM_FBGN2CGID = "ebi.biomart.dm.fbgn2cgid";

◆ PTH_EBI_BIOMART_HS_CE_ORTHOLOGY

string common.Paths.PTH_EBI_BIOMART_HS_CE_ORTHOLOGY = "ebi.biomart.hs.ce.orthologs";

◆ PTH_EBI_BIOMART_HS_DM_ORTHOLOGY

string common.Paths.PTH_EBI_BIOMART_HS_DM_ORTHOLOGY = "ebi.biomart.hs.dm.orthologs";

◆ PTH_EBI_BIOMART_HS_ENSG

string common.Paths.PTH_EBI_BIOMART_HS_ENSG = "ebi.biomart.hs.ensg";

◆ PTH_EBI_BIOMART_HS_ENSG2ENST

string common.Paths.PTH_EBI_BIOMART_HS_ENSG2ENST = "ebi.biomart.hs.e2enst";

◆ PTH_EBI_BIOMART_HS_ENSG2ENTREZ

string common.Paths.PTH_EBI_BIOMART_HS_ENSG2ENTREZ = "ebi.biomart.hs.e2entrez";

◆ PTH_EBI_BIOMART_HS_ENSG2HGNC

string common.Paths.PTH_EBI_BIOMART_HS_ENSG2HGNC = "ebi.biomart.hs.e2hgnc";

◆ PTH_EBI_BIOMART_HS_ENSG2UNIPROTSWISSPROT

string common.Paths.PTH_EBI_BIOMART_HS_ENSG2UNIPROTSWISSPROT = "ebi.biomart.hs.e2uniprotswissprot";

◆ PTH_EBI_BIOMART_HS_ENSG2UNIPROTTREMBL

string common.Paths.PTH_EBI_BIOMART_HS_ENSG2UNIPROTTREMBL = "ebi.biomart.hs.e2uniprottrembl";

◆ PTH_EBI_BIOMART_HS_ENST2CCDS

string common.Paths.PTH_EBI_BIOMART_HS_ENST2CCDS = "ebi.biomart.hs.enst2ccds";

◆ PTH_EBI_BIOMART_HS_ENST2ENSP

string common.Paths.PTH_EBI_BIOMART_HS_ENST2ENSP = "ebi.biomart.hs.enst2ensp";

◆ PTH_EBI_BIOMART_HS_MM_ORTHOLOGY

string common.Paths.PTH_EBI_BIOMART_HS_MM_ORTHOLOGY = "ebi.biomart.hs.mm.orthologs";

◆ PTH_EURAC_INTERNAL_GLOBAL_LD_1000G

string common.Paths.PTH_EURAC_INTERNAL_GLOBAL_LD_1000G = "eurac.internal.global.ld.1000G";

◆ PTH_GNF_HS_GENEATLAS

string common.Paths.PTH_GNF_HS_GENEATLAS = "gnf.hs.geneatlas";

◆ PTH_GO_GOA_HUMAN

string common.Paths.PTH_GO_GOA_HUMAN = "go.goa.human";

◆ PTH_GO_GRAPH_BP_POPULATED

string common.Paths.PTH_GO_GRAPH_BP_POPULATED = "go.graph.bp.populated";

◆ PTH_GO_GRAPH_CC_POPULATED

string common.Paths.PTH_GO_GRAPH_CC_POPULATED = "go.graph.cc.populated";

◆ PTH_GO_GRAPH_MF_POPULATED

string common.Paths.PTH_GO_GRAPH_MF_POPULATED = "go.graph.mf.populated";

◆ PTH_HGNC_BIOMART_HS_HGNC2ALIASES

string common.Paths.PTH_HGNC_BIOMART_HS_HGNC2ALIASES = "hgnc.biomart.hgnc2aliases";

◆ PTH_INTERACTION_MITAB

string common.Paths.PTH_INTERACTION_MITAB = "interactions.mitab"

◆ PTH_MISC_PHARMADME_COREMARKERS

string common.Paths.PTH_MISC_PHARMADME_COREMARKERS = "misc.pharmaadme.coremarkers";

◆ PTH_NCBI_CLINVAR_DAT

string common.Paths.PTH_NCBI_CLINVAR_DAT = "ncbi.clinvar.dat";

◆ PTH_REACTOME_BIOPAX

string common.Paths.PTH_REACTOME_BIOPAX = "reactome.biopax"

◆ PTH_UNIPROT_HS_ACCESSION2ENTRYNAME

string common.Paths.PTH_UNIPROT_HS_ACCESSION2ENTRYNAME = "uniprot.hs.accession2entryname";

◆ PTH_VDRC_R538_DM_TRFID2CGID

string common.Paths.PTH_VDRC_R538_DM_TRFID2CGID = "vdrc.r538.dm.trfid2cgid";

◆ PTH_VDRC_R57_DM_TRFID2CGID

string common.Paths.PTH_VDRC_R57_DM_TRFID2CGID = "vdrc.r57.dm.trfid2cgid";

◆ PTH_VDRC_R601_DM_TRFID2CGID

string common.Paths.PTH_VDRC_R601_DM_TRFID2CGID = "vdrc.r601.dm.trfid2cgid";

◆ PTH_WISHART_DRUGBANK_XML

string common.Paths.PTH_WISHART_DRUGBANK_XML = "wishart.drugbank.xml";

◆ PTH_WISHART_DRUGBANK_XSD

string common.Paths.PTH_WISHART_DRUGBANK_XSD = "wishart.drugbank.xsd";

Classes

Variables