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')
