def test_create_tables(self):
seed_data_util.create_tables(self.cursor)
self.cursor.execute(
'select count(*) from sqlite_master where type = ? and name = ?',
('table', 'seed_functional_roles'))
self.assertEqual(self.cursor.fetchone()[0], 1)
self.cursor.execute('SELECT COUNT(*) FROM seed_functional_roles')
self.assertEqual(self.cursor.fetchone()[0], 0)
self.cursor.execute(
'select count(*) from sqlite_master where type = ? and name = ?',
('table', 'seed_genomes'))
self.assertEqual(self.cursor.fetchone()[0], 1)
self.cursor.execute('SELECT COUNT(*) FROM seed_genomes')
self.assertEqual(self.cursor.fetchone()[0], 0)
self.cursor.execute(
'select count(*) from sqlite_master where type = ? and name = ?',
('table', 'seed_genes'))
self.assertEqual(self.cursor.fetchone()[0], 1)
self.cursor.execute('SELECT COUNT(*) FROM seed_genes')
self.assertEqual(self.cursor.fetchone()[0], 0)
self.cursor.execute(
'select count(*) from sqlite_master where type = ? and name = ?',
('table', 'seed_gene2role'))
self.assertEqual(self.cursor.fetchone()[0], 1)
self.cursor.execute('SELECT COUNT(*) FROM seed_gene2role')
self.assertEqual(self.cursor.fetchone()[0], 0)
def test_import_collection_tsv(self):
# Load test data
seed_data_util.create_tables(self.cursor)
seed_data_util.import_seed_functional_roles_table(
self.cursor, seed_roles_file)
self.cursor.execute(
'SELECT uid FROM seed_functional_roles WHERE seed_role_id IS ?',
('9724', ))
kegg_data_util.create_kegg_orthologs_table(self.cursor)
kegg_data_util.import_kegg_orthologs_list(
self.cursor, os.path.join(test_kegg_dir, 'kegg_ko_list.txt'))
self.cursor.execute('SELECT COUNT(*) FROM kegg_orthologs')
self.assertEqual(self.cursor.fetchone()[0], 1)
# Prepare database
db_utils.create_collections_table(self.cursor)
db_utils.create_collection2function_table(self.cursor)
# Import data
data_analysis.import_collection_tsv(self.cursor, collection_file,
'nitrogen_test', 'test info', '0')
# Check results
self.cursor.execute('SELECT COUNT(*) FROM collections')
self.assertEqual(self.cursor.fetchone()[0], 1)
self.cursor.execute('SELECT COUNT(*) FROM collection2function')
self.assertEqual(self.cursor.fetchone()[0], 4)
self.cursor.execute(
'SELECT name FROM collection2function WHERE function_uid=?', (2, ))
name = self.cursor.fetchone()[0]
self.assertIsNotNone(name)
self.assertEqual(name, 'Test_name2')
def test_fill_seed2kegg_mappings_table(self):
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)
seed_data_util.create_tables(self.cursor)
seed_data_util.import_seed_genomes(self.cursor, seed_genome_file)
seed_data_util.import_seed_genes(self.cursor, seed_gene_dir)
seed_data_util.create_seed2uniref_mappings_table(self.cursor)
seed_data_util.load_diamond_search_results(self.cursor,
seed_diamond_output, 95.0,
5)
self.cursor.execute('SELECT COUNT(*) FROM seed2uniref_mappings')
self.assertEqual(self.cursor.fetchone()[0], 3)
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'))
kegg_data_util.create_kegg2uniref_mappings_table(self.cursor)
kegg_data_util.load_diamond_search_results(self.cursor,
kegg_diamond_output, 95.0,
5)
self.cursor.execute('SELECT COUNT(*) FROM kegg2uniref_mappings')
self.assertEqual(self.cursor.fetchone()[0], 2)
seed_data_util.create_seed2kegg_mappings_table(self.cursor)
data_analysis.fill_seed2kegg_mappings_table(self.cursor,
seed2kegg_diamond_output,
95.0, 5)
self.cursor.execute('SELECT COUNT(*) FROM seed2kegg_mappings')
self.assertEqual(self.cursor.fetchone()[0], 4)
def test_import_seed_genomes(self):
seed_data_util.create_tables(self.cursor)
seed_data_util.import_seed_genomes(self.cursor, seed_genome_file)
self.cursor.execute(
'SELECT tax_id FROM seed_genomes WHERE seed_genome_id IS ?',
('511145.12', ))
self.assertEqual(self.cursor.fetchone()[0], u'511145')
self.cursor.execute('SELECT COUNT(*) FROM seed_genomes')
self.assertEqual(self.cursor.fetchone()[0], 4)
def test_import_seed_gene2roles_mapping(self):
seed_data_util.create_tables(self.cursor)
seed_data_util.import_seed_functional_roles_table(
self.cursor, seed_roles_file)
seed_data_util.import_seed_genomes(self.cursor, seed_genome_file)
seed_data_util.import_seed_genes(self.cursor, seed_gene_dir)
seed_data_util.import_seed_gene2roles_mapping(self.cursor,
seed_gene2roles_dir,
'test')
self.cursor.execute('SELECT COUNT(*) FROM seed_gene2role')
self.assertEqual(self.cursor.fetchone()[0], 6)
def test_find_seed2uniref_identical_mappings(self):
seed_data_util.create_tables(self.cursor)
seed_data_util.create_seed2uniref_mappings_table(self.cursor)
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)
seed_data_util.import_seed_genomes(self.cursor, seed_genome_file)
seed_data_util.import_seed_genes(self.cursor, seed_gene_dir)
data_analysis.find_seed2uniref_identical_mappings(self.cursor)
self.cursor.execute('SELECT COUNT(*) FROM seed2uniref_mappings')
self.assertEqual(self.cursor.fetchone()[0], 2)
def test_load_diamond_search_results(self):
seed_data_util.create_tables(self.cursor)
seed_data_util.create_seed2uniref_mappings_table(self.cursor)
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)
seed_data_util.import_seed_genomes(self.cursor, seed_genome_file)
seed_data_util.import_seed_genes(self.cursor, seed_gene_dir)
seed_data_util.load_diamond_search_results(self.cursor,
seed_diamond_file, 95.0, 5)
self.cursor.execute('SELECT COUNT(*) FROM seed2uniref_mappings')
self.assertEqual(self.cursor.fetchone()[0], 3)
def test_import_seed_functional_roles_table(self):
seed_data_util.create_tables(self.cursor)
seed_data_util.import_seed_functional_roles_table(
self.cursor, seed_roles_file)
self.cursor.execute(
'SELECT uid FROM seed_functional_roles WHERE seed_role_id IS ?',
('9724', ))
self.assertEqual(self.cursor.fetchone()[0], 6)
self.cursor.execute(
'SELECT COUNT(*) FROM seed_functional_roles WHERE seed_role_id IS ?',
('9724', ))
self.assertEqual(self.cursor.fetchone()[0], 1)
self.cursor.execute('SELECT COUNT(*) FROM seed_functional_roles')
self.assertEqual(self.cursor.fetchone()[0], 6)
def setUp(self):
self.conn = db_utils.connect_local_database(db_file)
self.cursor = self.conn.cursor()
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)
seed_data_util.create_tables(self.cursor)
seed_data_util.import_seed_functional_roles_table(
self.cursor, seed_roles_file)
seed_data_util.import_seed_genomes(self.cursor, seed_genome_file)
seed_data_util.import_seed_genes(self.cursor, seed_gene_dir)
seed_data_util.import_seed_gene2roles_mapping(self.cursor,
seed_gene2roles_dir,
'test')
seed_data_util.create_seed2uniref_mappings_table(self.cursor)
seed_data_util.load_diamond_search_results(self.cursor,
seed_diamond_output, 95.0,
5)
kegg_data_util.create_kegg_orthologs_table(self.cursor)
kegg_data_util.import_kegg_orthologs_list(
self.cursor, os.path.join(test_kegg_dir, 'kegg_ko_list.txt'))
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'))
kegg_data_util.create_kegg_genes2ko_table(self.cursor)
kegg_data_util.import_genes2ko_mappings(self.cursor, test_kegg_dir)
kegg_data_util.create_kegg2uniref_mappings_table(self.cursor)
kegg_data_util.load_diamond_search_results(self.cursor,
kegg_diamond_output, 95.0,
5)
seed_data_util.create_seed2kegg_mappings_table(self.cursor)
data_analysis.fill_seed2kegg_mappings_table(self.cursor,
seed2kegg_diamond_output,
95.0, 5)
db_utils.create_collections_table(self.cursor)
db_utils.create_collection2function_table(self.cursor)
data_analysis.import_collection_tsv(self.cursor, collection_file,
'nitrogen_test', 'test info', '0')
def main():
args = get_args()
# Open database and prepare tables
conn = db_utils.connect_local_database(args.db)
c = conn.cursor()
seed_data_util.drop_tables(c)
seed_data_util.drop_all_indices(c)
seed_data_util.create_tables(c)
# Import data
seed_data_util.import_seed_functional_roles_table(c,args.seed_roles_file)
seed_data_util.import_seed_genomes(c,args.seed_genome_file)
seed_data_util.import_seed_genes(c,args.seed_prot_dir)
seed_data_util.import_seed_gene2roles_mapping(c,args.seed_roles_dir,args.comment)
# Save changes and close database
conn.commit()
conn.close()
def test_export_kegg_unmapped_proteins(self):
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)
seed_data_util.create_tables(self.cursor)
seed_data_util.import_seed_genomes(self.cursor, seed_genome_file)
seed_data_util.import_seed_genes(self.cursor, seed_gene_dir)
seed_data_util.create_seed2uniref_mappings_table(self.cursor)
seed_data_util.load_diamond_search_results(self.cursor,
seed_diamond_output, 95.0,
5)
self.cursor.execute('SELECT COUNT(*) FROM seed2uniref_mappings')
self.assertEqual(self.cursor.fetchone()[0], 3)
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'))
kegg_data_util.create_kegg2uniref_mappings_table(self.cursor)
kegg_data_util.load_diamond_search_results(self.cursor,
kegg_diamond_output, 95.0,
5)
self.cursor.execute('SELECT COUNT(*) FROM kegg2uniref_mappings')
self.assertEqual(self.cursor.fetchone()[0], 2)
seed_data_util.create_seed2kegg_mappings_table(self.cursor)
data_analysis.fill_seed2kegg_mappings_table(self.cursor,
seed2kegg_diamond_output,
95.0, 5)
self.cursor.execute('SELECT COUNT(*) FROM seed2kegg_mappings')
self.assertEqual(self.cursor.fetchone()[0], 4)
data_analysis.export_kegg_unmapped_proteins(
self.cursor, os.path.join(test_kegg_dir, 'ko_proteins_nr.fasta'),
os.path.join(data_dir, 'out.fasta'))
with open(os.path.join(data_dir, 'out.fasta'), 'r') as f:
line = f.readline()
self.assertEqual(line[:15], '>dml:Dmul_28240')
f.closed
def test_get_role_uid(self):
seed_data_util.create_tables(self.cursor)
seed_data_util.import_seed_functional_roles_table(
self.cursor, seed_roles_file)
self.assertEqual(seed_data_util.get_role_uid(self.cursor, '105'), 1)
self.assertEqual(seed_data_util.get_role_uid(self.cursor, '2800'), 3)
def test_import_seed_genes(self):
seed_data_util.create_tables(self.cursor)
seed_data_util.import_seed_genomes(self.cursor, seed_genome_file)
seed_data_util.import_seed_genes(self.cursor, seed_gene_dir)
self.cursor.execute('SELECT COUNT(*) FROM seed_genes')
self.assertEqual(self.cursor.fetchone()[0], 8)