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Contents
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__),'..', '..', '..', '..', 'lib')) require 'rbbt/sources/biomart' require 'rbbt/sources/entrez' require File.join(File.dirname(__FILE__), '../../lib/helpers') $taxs = [10116] $scientific_name = "Rattus norvegicus" $biomart_db = 'rnorvegicus_gene_ensembl' $biomart_db_germline_variation = 'rnorvegicus_snp' $biomart_db_somatic_variation = 'rnorvegicus_snp_som' $ortholog_key = "rat_ensembl_gene" $biomart_lexicon = [ [ 'Associated Gene Name' , "external_gene_id"], [ 'HGNC symbol', "hgnc_symbol" ], [ 'HGNC automatic gene name', "hgnc_automatic_gene_name" ], [ 'HGNC curated gene name ', "hgnc_curated_gene_name" ], ] $biomart_identifiers = [ ['Entrez Gene ID', "entrezgene"], ['Associated Gene Name' , "rgd_symbol"], ['Protein ID' , "protein_id"] , ['UniProt/SwissProt ID' , "uniprot_swissprot"] , ['UniProt/SwissProt Accession' , "uniprot_swissprot_accession"] , ['RefSeq Protein ID' , "refseq_peptide"] , ['EMBL (Genbank) ID' , "embl"] , ['RGD ID' , "rgd"] , ['RGD Symbol' , "rgd_symbol"] , #['Affy rae230a', "affy_rae230a"], #['Affy rae230b', "affy_rae230b"], #['Affy RaGene', "affy_ragene_1_0_st_v1"], #['Affy rat230 2', "affy_rat230_2"], #['Affy RaEx', "affy_raex_1_0_st_v1"], #['Affy rg u34a', "affy_rg_u34a"], #['Affy rg u34b', "affy_rg_u34b"], #['Affy rg u34c', "affy_rg_u34c"], #['Affy rn u34', "affy_rn_u34"], #['Affy rt u34', "affy_rt_u34"], #['Codelink ID ', "codelink"], ] $namespace = File.basename(File.dirname(File.expand_path(__FILE__))) load File.join(File.dirname(__FILE__), '../organism_helpers.rb')
Version data entries
19 entries across 19 versions & 1 rubygems