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)
