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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 = [10090] $scientific_name = "Mus musculus" $ortholog_key = "mouse_ensembl_gene" $biomart_db = 'mmusculus_gene_ensembl' $biomart_db_germline_variation = 'mmusculus_snp' $biomart_db_somatic_variation = 'mmusculus_snp_som' $biomart_lexicon = [ [ 'Associated Gene Name' , "external_gene_name"], [ 'HGNC symbol', "hgnc_symbol" ], [ 'HGNC automatic gene name', "hgnc_automatic_gene_name" ], [ 'HGNC curated gene name ', "hgnc_curated_gene_name" ], ] $biomart_protein_identifiers = [ [ 'Protein ID', "protein_id" ], [ 'RefSeq Protein ID', "refseq_peptide" ], [ 'Unigene ID', "unigene" ], [ 'UniProt/SwissProt ID', "uniprot_swissprot" ], [ 'UniProt/SwissProt Accession', "uniprot_swissprot_accession" ], ] $biomart_probe_identifiers = [ ] $biomart_identifiers = [ [ 'Entrez Gene ID', "entrezgene"], [ 'Ensembl Protein ID', "ensembl_peptide_id" ], [ 'Associated Gene Name', "external_gene_name" ], [ 'CCDS ID', "ccds" ], [ 'Protein ID', "protein_id" ], [ 'RefSeq Protein ID', "refseq_peptide" ], [ 'Unigene ID', "unigene" ], [ 'UniProt/SwissProt ID', "uniprot_swissprot" ], [ 'UniProt/SwissProt Accession', "uniprot_swissprot_accession" ], [ 'EMBL (Genbank) ID' , "embl"] , ] $biomart_go= [ ["GO ID", 'go_id'], ["GO Namespace", 'namespace_1003'], ] $biomart_go_2009= [ ["GO BP ID", 'go_biological_process_id'], ["GO MF ID", 'go_molecular_function_id'], ["GO CC ID", 'go_cellular_component_id'], ] $namespace = File.basename(File.dirname(File.expand_path(__FILE__))) load File.join(File.dirname(__FILE__), '../organism_helpers.rb')
Version data entries
7 entries across 7 versions & 1 rubygems