def main(): args = get_args() # Open database conn = db_utils.connect_local_database(args.seed_db) c = conn.cursor() db_utils.attach_local_database(c, args.uniref_db, 'uniref_proteins') # Prepare database print('Drop seed2uniref_mappings table...') seed_data_util.drop_seed2uniref_mappings_table(c) print('Create seed2uniref_mappings table...') seed_data_util.create_seed2uniref_mappings_table(c) # Import data print('Find genes with identical hashes...') data_analysis.find_seed2uniref_identical_mappings(c) print('Get genes from DIAMOND output...') seed_data_util.load_diamond_search_results(c, args.diamond_out, 95.0, 5) # Write changes and close database print('Saving database...', end='') conn.commit() conn.close() print('done.')
def setUp(self): self.conn = db_utils.connect_local_database(seed_db_file) self.cursor = self.conn.cursor() seed_data_util.create_seed_genomes_table(self.cursor) seed_data_util.import_seed_genomes(self.cursor, os.path.join(data_dir, 'test_seed_genomes.txt')) seed_data_util.create_seed_genes_table(self.cursor) seed_data_util.import_seed_genes(self.cursor, test_seed_dir) db_utils.attach_local_database(self.cursor, uniref_db_file, 'uniref_proteins') uniref_data_util.create_uniref_proteins_table(self.cursor) uniref_data_util.import_uniref_fasta(self.cursor, uniref_fasta_file) uniref_data_util.create_uniref_proteins_indices(self.cursor)
def main(): args = get_args() # Open database conn = db_utils.connect_local_database(args.kegg_db) c = conn.cursor() db_utils.attach_local_database(c, args.seed_db, 'seed_data') print('Finding unmapped proteins...') data_analysis.export_kegg_unmapped_proteins(c, args.infile, args.outfile) conn.close() print('done.')
def main(): args = get_args() # Open database conn = db_utils.connect_local_database(args.seed_db) c = conn.cursor() db_utils.attach_local_database(c, args.kegg_db, 'kegg_data') print ('Finding genes...') gene_collection = data_analysis.make_collection_gene_list(c, args.name, args.ver) print(len(gene_collection), 'genes found. Writing output...') data_analysis.export_collection_proteins(gene_collection,args.seed_prots,args.outfile) data_analysis.export_collection_proteins(gene_collection,args.kegg_prots,args.outfile) conn.close() print ('done.')
def main(): args = get_args() # Open database conn = db_utils.connect_local_database(args.seed_db) c = conn.cursor() db_utils.attach_local_database(c, args.kegg_db, 'kegg_data') db_utils.create_collections_table(c) db_utils.create_collection2function_table(c) data_analysis.import_collection_tsv(c, args.infile, args.name, args.info, args.ver) conn.commit() conn.close() print('done.')
def setUp(self): self.conn = db_utils.connect_local_database( os.path.join(data_dir, kegg_db_file)) self.cursor = self.conn.cursor() db_utils.attach_local_database(self.cursor, os.path.join(data_dir, uniref_db_file), 'uniref_proteins') kegg_data_util.create_kegg_genomes_table(self.cursor) kegg_data_util.import_kegg_genomes_list( self.cursor, os.path.join(test_kegg_dir, 'kegg_genomes.txt')) kegg_data_util.create_kegg_genes_table(self.cursor) kegg_data_util.import_kegg_genes( self.cursor, os.path.join(test_kegg_dir, 'ko_proteins_nr.fasta')) uniref_data_util.create_uniref_proteins_table(self.cursor) uniref_data_util.import_uniref_fasta(self.cursor, uniref_fasta_file) uniref_data_util.create_uniref_proteins_indices(self.cursor)
def main(): args = get_args() # Open database conn = db_utils.connect_local_database(args.seed_db) c = conn.cursor() db_utils.attach_local_database(c, args.kegg_db, 'kegg_data') db_utils.attach_local_database(c, args.uniref_db, 'uniref_proteins') # Prepare database seed_data_util.drop_seed2kegg_mappings_table(c) print('Creating seed2kegg_mappings table...') seed_data_util.create_seed2kegg_mappings_table(c) print('Populating seed2kegg_mappings table...') data_analysis.fill_seed2kegg_mappings_table(c, args.diamond_out, 95.0, 5) # Write changes and close database print('Saving database...', end='') conn.commit() conn.close() print('done.')
def setUp(self): self.conn = db_utils.connect_local_database(db_file) self.cursor = self.conn.cursor() db_utils.attach_local_database(self.cursor, uniref_db_file, 'uniref_proteins')