def test_entrez_source ( self ) : """ Test BioSeqs.from_entrez() method and len() property. """ query = '"h**o sapiens"[porgn] AND mitochondrion[Filter] AND ' \ 'mRNA[Filter]' seq_db = BioSeqs.from_entrez(entrez_db='nuccore', query=query, email='*****@*****.**', max_fetch=10) # Check the number of sequences fetched self.assertEqual(len(seq_db), 10) # Check report information self.assertIn('entrez', seq_db._report[0][1]) self.assertIn('nuccore', seq_db._report[0][2]) self.assertIn(query, seq_db._report[0][3])
def test_entrez_source(self): """ Test BioSeqs.from_entrez() method and len() property. """ query = '"h**o sapiens"[porgn] AND mitochondrion[Filter] AND ' \ 'mRNA[Filter]' seq_db = BioSeqs.from_entrez(entrez_db='nuccore', query=query, email='*****@*****.**', max_fetch=10) # Check the number of sequences fetched self.assertEqual(len(seq_db), 10) # Check report information self.assertIn('entrez', seq_db._report[0][1]) self.assertIn('nuccore', seq_db._report[0][2]) self.assertIn(query, seq_db._report[0][3])
def test_update ( self ) : """ Test BioSeqs.update() method. """ query = '"h**o sapiens"[porgn] AND mitochondrion[Filter] AND ' \ 'mRNA[Filter]' seq_db = BioSeqs.from_entrez(entrez_db='nuccore', email='*****@*****.**', query=query, max_fetch=10) # Check the number of sequences fetched self.assertEqual(len(seq_db), 10) # Update the database fetching all the available sequences seq_db.update('*****@*****.**') # Check the number of sequences fetched handle = Entrez.esearch(db='nuccore', term=query, rettype='count') num_seqs = int(Entrez.read(handle)['Count']) self.assertEqual(len(seq_db), num_seqs)
def test_update(self): """ Test BioSeqs.update() method. """ query = '"h**o sapiens"[porgn] AND mitochondrion[Filter] AND ' \ 'mRNA[Filter]' seq_db = BioSeqs.from_entrez(entrez_db='nuccore', email='*****@*****.**', query=query, max_fetch=10) # Check the number of sequences fetched self.assertEqual(len(seq_db), 10) # Update the database fetching all the available sequences seq_db.update('*****@*****.**') # Check the number of sequences fetched handle = Entrez.esearch(db='nuccore', term=query, rettype='count') num_seqs = int(Entrez.read(handle)['Count']) self.assertEqual(len(seq_db), num_seqs)