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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Dealing with storage of biopython objects in a BioSQL relational db."""
from __future__ import print_function
import os
import platform
import sys
import tempfile
import time
import unittest
try:
import configparser # Python 3
except ImportError:
import ConfigParser as configparser # Python 2
from Bio._py3k import StringIO
from Bio._py3k import zip
from Bio._py3k import basestring
# Hide annoying warnings from things like bonds in GenBank features,
# or PostgreSQL schema rules. TODO - test these warnings are raised!
import warnings
from Bio import BiopythonWarning
# local stuff
from Bio import MissingExternalDependencyError
from Bio.Seq import Seq, MutableSeq
from Bio.SeqFeature import SeqFeature, UnknownPosition, ExactPosition
from Bio import Alphabet
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from BioSQL import BioSeqDatabase
from BioSQL import BioSeq
from seq_tests_common import compare_record, compare_records
if __name__ == "__main__":
raise RuntimeError("Call this via test_BioSQL_*.py not directly")
# Exporting these to the test_BioSQL_XXX.py files which import this file:
# DBDRIVER, DBTYPE, DBHOST, DBUSER, DBPASSWD, TESTDB, DBSCHEMA, SQL_FILE, SYSTEM
SYSTEM = platform.system()
def load_biosql_ini(DBTYPE):
"""Load the database settings from INI file."""
if not os.path.isfile("biosql.ini"):
raise MissingExternalDependencyError("BioSQL test configuration"
" file biosql.ini missing"
" (see biosql.ini.sample)")
config = configparser.ConfigParser()
config.read("biosql.ini")
DBHOST = config.get(DBTYPE, "dbhost")
DBUSER = config.get(DBTYPE, "dbuser")
DBPASSWD = config.get(DBTYPE, "dbpasswd")
TESTDB = config.get(DBTYPE, "testdb")
return DBHOST, DBUSER, DBPASSWD, TESTDB
def temp_db_filename():
"""Generate a temporary filename for SQLite database."""
# In memory SQLite does not work with current test structure since the tests
# expect databases to be retained between individual tests.
# TESTDB = ':memory:'
# Instead, we use (if we can) /dev/shm
try:
h, test_db_fname = tempfile.mkstemp("_BioSQL.db", dir='/dev/shm')
except OSError:
# We can't use /dev/shm
h, test_db_fname = tempfile.mkstemp("_BioSQL.db")
os.close(h)
return test_db_fname
def check_config(dbdriver, dbtype, dbhost, dbuser, dbpasswd, testdb):
"""Verify the database settings work for connecting."""
global DBDRIVER, DBTYPE, DBHOST, DBUSER, DBPASSWD, TESTDB, DBSCHEMA
global SYSTEM, SQL_FILE
DBDRIVER = dbdriver
DBTYPE = dbtype
DBHOST = dbhost
DBUSER = dbuser
DBPASSWD = dbpasswd
TESTDB = testdb
if not DBDRIVER or not DBTYPE or not DBUSER:
# No point going any further...
raise MissingExternalDependencyError("Incomplete BioSQL test settings")
# Check the database driver is installed:
if SYSTEM == "Java":
try:
if DBDRIVER in ["MySQLdb"]:
import com.mysql.jdbc.Driver
elif DBDRIVER in ["psycopg2"]:
import org.postgresql.Driver
except ImportError:
message = "Install the JDBC driver for %s to use BioSQL " % DBTYPE
raise MissingExternalDependencyError(message)
else:
try:
__import__(DBDRIVER)
except ImportError:
message = "Install %s if you want to use %s with BioSQL " % (DBDRIVER, DBTYPE)
raise MissingExternalDependencyError(message)
try:
if DBDRIVER in ["sqlite3"]:
server = BioSeqDatabase.open_database(driver=DBDRIVER, db=TESTDB)
else:
server = BioSeqDatabase.open_database(driver=DBDRIVER, host=DBHOST,
user=DBUSER, passwd=DBPASSWD)
server.close()
del server
except Exception as e:
message = "Connection failed, check settings if you plan to use BioSQL: %s" % e
raise MissingExternalDependencyError(message)
DBSCHEMA = "biosqldb-" + DBTYPE + ".sql"
SQL_FILE = os.path.join(os.getcwd(), "BioSQL", DBSCHEMA)
if not os.path.isfile(SQL_FILE):
message = "Missing SQL schema file: %s" % SQL_FILE
raise MissingExternalDependencyError(message)
def _do_db_create():
"""Do the actual work of database creation.
Relevant for MySQL and PostgreSQL.
"""
# first open a connection to create the database
server = BioSeqDatabase.open_database(driver=DBDRIVER, host=DBHOST,
user=DBUSER, passwd=DBPASSWD)
if DBDRIVER == "pgdb":
# The pgdb postgres driver does not support autocommit, so here we
# commit the current transaction so that 'drop database' query will
# be outside a transaction block
server.adaptor.cursor.execute("COMMIT")
else:
# Auto-commit: postgresql cannot drop database in a transaction
try:
server.adaptor.autocommit()
except AttributeError:
pass
# drop anything in the database
try:
# with Postgres, can get errors about database still being used and
# not able to be dropped. Wait briefly to be sure previous tests are
# done with it.
time.sleep(1)
sql = r"DROP DATABASE " + TESTDB
server.adaptor.cursor.execute(sql, ())
except (server.module.OperationalError,
server.module.Error,
server.module.DatabaseError) as e: # the database doesn't exist
pass
except (server.module.IntegrityError,
server.module.ProgrammingError) as e: # ditto--perhaps
if str(e).find('database "%s" does not exist' % TESTDB) == -1:
server.close()
raise
# create a new database
sql = r"CREATE DATABASE " + TESTDB
server.adaptor.execute(sql, ())
server.close()
def create_database():
"""Delete any existing BioSQL test DB, then (re)create an empty BioSQL DB.
Returns TESTDB name which will change for for SQLite.
"""
if DBDRIVER in ["sqlite3"]:
global TESTDB
if os.path.exists(TESTDB):
try:
os.remove(TESTDB)
except Exception:
time.sleep(1)
try:
os.remove(TESTDB)
except Exception:
# Seen this with PyPy 2.1 (and older) on Windows -
# which suggests an open handle still exists?
print("Could not remove %r" % TESTDB)
pass
# Now pick a new filename - just in case there is a stale handle
# (which might be happening under Windows...)
TESTDB = temp_db_filename()
else:
_do_db_create()
# now open a connection to load the database
server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER, passwd=DBPASSWD,
host=DBHOST, db=TESTDB)
try:
server.load_database_sql(SQL_FILE)
server.commit()
server.close()
except Exception:
# Failed, but must close the handle...
server.close()
raise
return TESTDB
def destroy_database():
"""Delete any temporary BioSQL sqlite3 database files."""
if DBDRIVER in ["sqlite3"]:
if os.path.exists(TESTDB):
os.remove(TESTDB)
def load_database(gb_filename_or_handle):
"""Load a GenBank file into a new BioSQL database.
This is useful for running tests against a newly created database.
"""
TESTDB = create_database()
# now open a connection to load the database
db_name = "biosql-test"
server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER, passwd=DBPASSWD,
host=DBHOST, db=TESTDB)
db = server.new_database(db_name)
# get the GenBank file we are going to put into it
iterator = SeqIO.parse(gb_filename_or_handle, "gb")
# finally put it in the database
count = db.load(iterator)
server.commit()
server.close()
return count
def load_multi_database(gb_filename_or_handle, gb_filename_or_handle2):
"""Load two GenBank files into a new BioSQL database as different subdatabases.
This is useful for running tests against a newly created database.
"""
TESTDB = create_database()
# now open a connection to load the database
db_name = "biosql-test"
db_name2 = "biosql-test2"
server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER, passwd=DBPASSWD,
host=DBHOST, db=TESTDB)
db = server.new_database(db_name)
# get the GenBank file we are going to put into it
iterator = SeqIO.parse(gb_filename_or_handle, "gb")
count = db.load(iterator)
db = server.new_database(db_name2)
# get the GenBank file we are going to put into it
iterator = SeqIO.parse(gb_filename_or_handle2, "gb")
# finally put it in the database
count2 = db.load(iterator)
server.commit()
server.close()
return count + count2
class MultiReadTest(unittest.TestCase):
"""Test reading a database with multiple namespaces."""
loaded_db = 0
def setUp(self):
"""Connect to and load up the database."""
load_multi_database("GenBank/cor6_6.gb", "GenBank/NC_000932.gb")
self.server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER,
passwd=DBPASSWD,
host=DBHOST,
db=TESTDB)
self.db = self.server["biosql-test"]
self.db2 = self.server['biosql-test2']
def tearDown(self):
self.server.close()
destroy_database()
del self.db
del self.db2
del self.server
def test_server(self):
"""Check BioSeqDatabase methods."""
server = self.server
self.assertIn("biosql-test", server)
self.assertIn("biosql-test2", server)
self.assertEqual(2, len(server))
self.assertEqual(["biosql-test", 'biosql-test2'], list(server.keys()))
# Check we can delete the namespace...
del server["biosql-test"]
del server["biosql-test2"]
self.assertEqual(0, len(server))
try:
del server["non-existant-name"]
assert False, "Should have raised KeyError"
except KeyError:
pass
def test_get_db_items(self):
"""Check list, keys, length etc."""
db = self.db
items = list(db.values())
keys = list(db)
l = len(items)
self.assertEqual(l, len(db))
self.assertEqual(l, len(list(db)))
self.assertEqual(l, len(list(db.items())))
self.assertEqual(l, len(list(db.keys())))
self.assertEqual(l, len(list(db.values())))
if sys.version_info[0] == 2:
# Check legacy methods for Python 2 as well:
self.assertEqual(l, len(list(db.iteritems())))
self.assertEqual(l, len(list(db.iterkeys())))
self.assertEqual(l, len(list(db.itervalues())))
for (k1, r1), (k2, r2) in zip(zip(keys, items), db.items()):
self.assertEqual(k1, k2)
self.assertEqual(r1.id, r2.id)
for k in keys:
del db[k]
self.assertEqual(0, len(db))
try:
del db["non-existant-name"]
assert False, "Should have raised KeyError"
except KeyError:
pass
def test_cross_retrieval_of_items(self):
"""Test that valid ids can't be retrieved between namespaces."""
db = self.db
db2 = self.db2
for db2_id in db2.keys():
try:
rec = db[db2_id]
assert False, "Should have raised KeyError"
except KeyError:
pass
class ReadTest(unittest.TestCase):
"""Test reading a database from an already built database."""
loaded_db = 0
def setUp(self):
"""Connect to and load up the database."""
load_database("GenBank/cor6_6.gb")
self.server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER,
passwd=DBPASSWD,
host=DBHOST,
db=TESTDB)
self.db = self.server["biosql-test"]
def tearDown(self):
self.server.close()
destroy_database()
del self.db
del self.server
def test_server(self):
"""Check BioSeqDatabase methods."""
server = self.server
self.assertIn("biosql-test", server)
self.assertEqual(1, len(server))
self.assertEqual(["biosql-test"], list(server.keys()))
# Check we can delete the namespace...
del server["biosql-test"]
self.assertEqual(0, len(server))
try:
del server["non-existant-name"]
assert False, "Should have raised KeyError"
except KeyError:
pass
def test_get_db_items(self):
"""Check list, keys, length etc."""
db = self.db
items = list(db.values())
keys = list(db)
l = len(items)
self.assertEqual(l, len(db))
self.assertEqual(l, len(list(db.items())))
self.assertEqual(l, len(list(db)))
self.assertEqual(l, len(list(db.values())))
for (k1, r1), (k2, r2) in zip(zip(keys, items), db.items()):
self.assertEqual(k1, k2)
self.assertEqual(r1.id, r2.id)
for k in keys:
del db[k]
self.assertEqual(0, len(db))
try:
del db["non-existant-name"]
assert False, "Should have raised KeyError"
except KeyError:
pass
def test_lookup_items(self):
"""Test retrieval of items using various ids."""
self.db.lookup(accession="X62281")
try:
self.db.lookup(accession="Not real")
raise AssertionError("No problem on fake id retrieval")
except IndexError:
pass
self.db.lookup(display_id="ATKIN2")
try:
self.db.lookup(display_id="Not real")
raise AssertionError("No problem on fake id retrieval")
except IndexError:
pass
# primary id retrieval
self.db.lookup(primary_id="16353")
try:
self.db.lookup(primary_id="Not Real")
raise AssertionError("No problem on fake primary id retrieval")
except IndexError:
pass
class SeqInterfaceTest(unittest.TestCase):
"""Make sure the BioSQL objects implement the expected biopython interface."""
def setUp(self):
"""Load a database."""
load_database("GenBank/cor6_6.gb")
self.server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER, passwd=DBPASSWD,
host=DBHOST, db=TESTDB)
self.db = self.server["biosql-test"]
self.item = self.db.lookup(accession="X62281")
def tearDown(self):
self.server.close()
destroy_database()
del self.db
del self.item
del self.server
def test_seq_record(self):
"""Make sure SeqRecords from BioSQL implement the right interface."""
test_record = self.item
self.assertTrue(isinstance(test_record.seq, BioSeq.DBSeq))
self.assertEqual(test_record.id, "X62281.1", test_record.id)
self.assertEqual(test_record.name, "ATKIN2")
self.assertEqual(test_record.description, "A.thaliana kin2 gene")
self.assertTrue(hasattr(test_record, 'annotations'))
# XXX should do something with annotations once they are like
# a dictionary
for feature in test_record.features:
self.assertTrue(isinstance(feature, SeqFeature))
# shouldn't cause any errors!
self.assertTrue(isinstance(str(test_record), basestring))
# Confirm can delete annotations etc to test these properties
del test_record.annotations
del test_record.dbxrefs
del test_record.features
del test_record.seq
def test_seq(self):
"""Make sure Seqs from BioSQL implement the right interface."""
test_seq = self.item.seq
alphabet = test_seq.alphabet
self.assertTrue(isinstance(alphabet, Alphabet.Alphabet))
data = test_seq.data
self.assertEqual(type(data), type(""))
string_rep = str(test_seq)
self.assertEqual(string_rep, str(test_seq)) # check __str__ too
self.assertEqual(type(string_rep), type(""))
self.assertEqual(len(test_seq), 880)
self.assertEqual(test_seq[879], "A")
self.assertEqual(test_seq[-1], "A")
self.assertEqual(test_seq[0], "A")
self.assertEqual(test_seq[-880], "A")
self.assertRaises(IndexError, test_seq.__getitem__, 880)
self.assertRaises(IndexError, test_seq.__getitem__, -881)
self.assertRaises(TypeError, test_seq.__getitem__, None)
def test_convert(self):
"""Check can turn a DBSeq object into a Seq or MutableSeq."""
test_seq = self.item.seq
other = test_seq.toseq()
self.assertEqual(str(test_seq), str(other))
self.assertEqual(test_seq.alphabet, other.alphabet)
self.assertTrue(isinstance(other, Seq))
other = test_seq.tomutable()
self.assertEqual(str(test_seq), str(other))
self.assertEqual(test_seq.alphabet, other.alphabet)
self.assertTrue(isinstance(other, MutableSeq))
def test_addition(self):
"""Check can add DBSeq objects together."""
test_seq = self.item.seq
for other in [Seq("ACGT", test_seq.alphabet),
MutableSeq("ACGT", test_seq.alphabet),
"ACGT",
test_seq]:
test = test_seq + other
self.assertEqual(str(test), str(test_seq) + str(other))
self.assertTrue(isinstance(test, Seq))
test = other + test_seq
self.assertEqual(str(test), str(other) + str(test_seq))
def test_seq_slicing(self):
"""Check that slices of sequences are retrieved properly."""
test_seq = self.item.seq
new_seq = test_seq[:10]
self.assertTrue(isinstance(new_seq, BioSeq.DBSeq))
# simple slicing
self.assertEqual(str(test_seq[:5]), 'ATTTG')
self.assertEqual(str(test_seq[0:5]), 'ATTTG')
self.assertEqual(str(test_seq[2:3]), 'T')
self.assertEqual(str(test_seq[2:4]), 'TT')
self.assertEqual(str(test_seq[870:]), 'TTGAATTATA')
# getting more fancy
self.assertEqual(test_seq[-1], 'A')
self.assertEqual(test_seq[1], 'T')
self.assertEqual(str(test_seq[-10:][5:]), "TTATA")
self.assertEqual(str(test_seq[-10:][5:]), "TTATA")
def test_record_slicing(self):
"""Check that slices of DBSeqRecord are retrieved properly."""
new_rec = self.item[400:]
self.assertTrue(isinstance(new_rec, SeqRecord))
self.assertEqual(len(new_rec), 480)
self.assertEqual(len(new_rec.features), 5)
def test_seq_features(self):
"""Check SeqFeatures of a sequence."""
test_features = self.item.features
cds_feature = test_features[6]
self.assertEqual(cds_feature.type, "CDS")
self.assertEqual(str(cds_feature.location),
"join{[103:160](+), [319:390](+), [503:579](+)}")
try:
self.assertEqual(cds_feature.qualifiers["gene"], ["kin2"])
self.assertEqual(cds_feature.qualifiers["protein_id"], ["CAA44171.1"])
self.assertEqual(cds_feature.qualifiers["codon_start"], ["1"])
except KeyError:
raise KeyError("Missing expected entries, have %s"
% repr(cds_feature.qualifiers))
self.assertIn("db_xref", cds_feature.qualifiers)
multi_ann = cds_feature.qualifiers["db_xref"]
self.assertEqual(len(multi_ann), 2)
self.assertIn("GI:16354", multi_ann)
self.assertIn("SWISS-PROT:P31169", multi_ann)
class LoaderTest(unittest.TestCase):
"""Load a database from a GenBank file."""
def setUp(self):
# create TESTDB
TESTDB = create_database()
# load the database
db_name = "biosql-test"
self.server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER, passwd=DBPASSWD,
host=DBHOST, db=TESTDB)
# remove the database if it already exists
try:
self.server[db_name]
self.server.remove_database(db_name)
except KeyError:
pass
self.db = self.server.new_database(db_name)
# get the GenBank file we are going to put into it
self.iterator = SeqIO.parse("GenBank/cor6_6.gb", "gb")
def tearDown(self):
self.server.close()
destroy_database()
del self.db
del self.server
def test_load_database(self):
"""Load SeqRecord objects into a BioSQL database."""
self.db.load(self.iterator)
# do some simple tests to make sure we actually loaded the right
# thing. More advanced tests in a different module.
items = list(self.db.values())
self.assertEqual(len(items), 6)
self.assertEqual(len(self.db), 6)
item_names = []
item_ids = []
for item in items:
item_names.append(item.name)
item_ids.append(item.id)
item_names.sort()
item_ids.sort()
self.assertEqual(item_names, ['AF297471', 'ARU237582', 'ATCOR66M',
'ATKIN2', 'BNAKINI', 'BRRBIF72'])
self.assertEqual(item_ids, ['AF297471.1', 'AJ237582.1', 'L31939.1',
'M81224.1', 'X55053.1', 'X62281.1'])
class DeleteTest(unittest.TestCase):
"""Test proper deletion of entries from a database."""
loaded_db = 0
def setUp(self):
"""Connect to and load up the database."""
load_database("GenBank/cor6_6.gb")
self.server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER,
passwd=DBPASSWD,
host=DBHOST,
db=TESTDB)
self.db = self.server["biosql-test"]
def tearDown(self):
self.server.close()
destroy_database()
del self.db
del self.server
def test_server(self):
"""Check BioSeqDatabase methods."""
server = self.server
self.assertIn("biosql-test", server)
self.assertEqual(1, len(server))
self.assertEqual(["biosql-test"], list(server.keys()))
# Check we can delete the namespace...
del server["biosql-test"]
self.assertEqual(0, len(server))
try:
del server["non-existant-name"]
assert False, "Should have raised KeyError"
except KeyError:
pass
def test_del_db_items(self):
"""Check all associated data is deleted from an item."""
db = self.db
items = list(db.values())
keys = list(db)
l = len(items)
for seq_id in self.db.keys():
sql = "SELECT seqfeature_id from seqfeature where bioentry_id = '%s'"
# get the original number of seqfeatures associated with the bioentry
seqfeatures = self.db.adaptor.execute_and_fetchall(sql % (seq_id))
del db[seq_id]
# check to see that the entry in the bioentry table is removed
self.assertEqual(seq_id in db, False)
# no need to check seqfeature presence if it had none to begin with
if len(seqfeatures):
rows_d = self.db.adaptor.execute_and_fetchall(sql % (seq_id))
# check to see that associated data is removed
self.assertEqual(len(rows_d), 0)
class DupLoadTest(unittest.TestCase):
"""Check a few duplicate conditions fail."""
def setUp(self):
# drop any old database and create a new one:
TESTDB = create_database()
# connect to new database:
self.server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER, passwd=DBPASSWD,
host=DBHOST, db=TESTDB)
# Create new namespace within new empty database:
self.db = self.server.new_database("biosql-test")
def tearDown(self):
self.server.rollback()
self.server.close()
destroy_database()
del self.db
del self.server
def test_duplicate_load(self):
"""Make sure can't import a single record twice (in one go)."""
record = SeqRecord(Seq("ATGCTATGACTAT", Alphabet.generic_dna),
id="Test1")
try:
count = self.db.load([record, record])
except Exception as err:
# Good!
# Note we don't do a specific exception handler because the
# exception class will depend on which DB back end is in use.
self.assertTrue(err.__class__.__name__ in ["IntegrityError",
"AttributeError",
"OperationalError"],
err.__class__.__name__)
return
raise Exception("Should have failed! Loaded %i records" % count)
def test_duplicate_load2(self):
"""Make sure can't import a single record twice (in steps)."""
record = SeqRecord(Seq("ATGCTATGACTAT", Alphabet.generic_dna),
id="Test2")
count = self.db.load([record])
self.assertEqual(count, 1)
try:
count = self.db.load([record])
except Exception as err:
# Good!
self.assertTrue(err.__class__.__name__ in ["IntegrityError",
"AttributeError"],
err.__class__.__name__)
return
raise Exception("Should have failed! Loaded %i records" % count)
def test_duplicate_id_load(self):
"""Make sure can't import records with same ID (in one go)."""
record1 = SeqRecord(Seq("ATGCTATGACTAT", Alphabet.generic_dna),
id="TestA")
record2 = SeqRecord(Seq("GGGATGCGACTAT", Alphabet.generic_dna),
id="TestA")
try:
count = self.db.load([record1, record2])
except Exception as err:
# Good!
self.assertTrue(err.__class__.__name__ in ["IntegrityError",
"AttributeError"],
err.__class__.__name__)
return
raise Exception("Should have failed! Loaded %i records" % count)
class ClosedLoopTest(unittest.TestCase):
"""Test file -> BioSQL -> file."""
@classmethod
def setUpClass(cls):
# NOTE - For speed I don't bother to create a new database each time,
# simply a new unique namespace is used for each test.
TESTDB = create_database()
def test_NC_005816(self):
"""From GenBank file to BioSQL and back to a GenBank file, NC_005816."""
with warnings.catch_warnings():
# BiopythonWarning: order location operators are not fully supported
warnings.simplefilter('ignore', BiopythonWarning)
self.loop("GenBank/NC_005816.gb", "gb")
def test_NC_000932(self):
"""From GenBank file to BioSQL and back to a GenBank file, NC_000932."""
self.loop("GenBank/NC_000932.gb", "gb")
def test_NT_019265(self):
"""From GenBank file to BioSQL and back to a GenBank file, NT_019265."""
self.loop("GenBank/NT_019265.gb", "gb")
def test_protein_refseq2(self):
"""From GenBank file to BioSQL and back to a GenBank file, protein_refseq2."""
with warnings.catch_warnings():
# BiopythonWarning: order location operators are not fully supported
warnings.simplefilter('ignore', BiopythonWarning)
self.loop("GenBank/protein_refseq2.gb", "gb")
def test_no_ref(self):
"""From GenBank file to BioSQL and back to a GenBank file, noref."""
self.loop("GenBank/noref.gb", "gb")
def test_one_of(self):
"""From GenBank file to BioSQL and back to a GenBank file, one_of."""
self.loop("GenBank/one_of.gb", "gb")
def test_cor6_6(self):
"""From GenBank file to BioSQL and back to a GenBank file, cor6_6."""
self.loop("GenBank/cor6_6.gb", "gb")
def test_arab1(self):
"""From GenBank file to BioSQL and back to a GenBank file, arab1."""
self.loop("GenBank/arab1.gb", "gb")
def loop(self, filename, format):
original_records = list(SeqIO.parse(filename, format))
# now open a connection to load the database
server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER, passwd=DBPASSWD,
host=DBHOST, db=TESTDB)
db_name = "test_loop_%s" % filename # new namespace!
db = server.new_database(db_name)
count = db.load(original_records)
self.assertEqual(count, len(original_records))
server.commit()
# Now read them back...
biosql_records = [db.lookup(name=rec.name)
for rec in original_records]
# And check they agree
self.assertTrue(compare_records(original_records, biosql_records))
# Now write to a handle...
handle = StringIO()
SeqIO.write(biosql_records, handle, "gb")
# Now read them back...
handle.seek(0)
new_records = list(SeqIO.parse(handle, "gb"))
# And check they still agree
self.assertEqual(len(new_records), len(original_records))
for old, new in zip(original_records, new_records):
# TODO - remove this hack because we don't yet write these (yet):
for key in ["comment", "references", "db_source"]:
if key in old.annotations and key not in new.annotations:
del old.annotations[key]
self.assertTrue(compare_record(old, new))
# Done
handle.close()
server.close()
class TransferTest(unittest.TestCase):
"""Test file -> BioSQL, BioSQL -> BioSQL."""
# NOTE - For speed I don't bother to create a new database each time,
# simply a new unique namespace is used for each test.
def setUp(self):
TESTDB = create_database()
def test_NC_005816(self):
"""From GenBank file to BioSQL, then again to a new namespace, NC_005816."""
with warnings.catch_warnings():
# BiopythonWarning: order location operators are not fully supported
warnings.simplefilter('ignore', BiopythonWarning)
self.trans("GenBank/NC_005816.gb", "gb")
def test_NC_000932(self):
"""From GenBank file to BioSQL, then again to a new namespace, NC_000932."""
self.trans("GenBank/NC_000932.gb", "gb")
def test_NT_019265(self):
"""From GenBank file to BioSQL, then again to a new namespace, NT_019265."""
self.trans("GenBank/NT_019265.gb", "gb")
def test_protein_refseq2(self):
"""From GenBank file to BioSQL, then again to a new namespace, protein_refseq2."""
with warnings.catch_warnings():
# BiopythonWarning: order location operators are not fully supported
warnings.simplefilter('ignore', BiopythonWarning)
self.trans("GenBank/protein_refseq2.gb", "gb")
def test_no_ref(self):
"""From GenBank file to BioSQL, then again to a new namespace, noref."""
self.trans("GenBank/noref.gb", "gb")
def test_one_of(self):
"""From GenBank file to BioSQL, then again to a new namespace, one_of."""
self.trans("GenBank/one_of.gb", "gb")
def test_cor6_6(self):
"""From GenBank file to BioSQL, then again to a new namespace, cor6_6."""
self.trans("GenBank/cor6_6.gb", "gb")
def test_arab1(self):
"""From GenBank file to BioSQL, then again to a new namespace, arab1."""
self.trans("GenBank/arab1.gb", "gb")
def trans(self, filename, format):
original_records = list(SeqIO.parse(filename, format))
# now open a connection to load the database
server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER, passwd=DBPASSWD,
host=DBHOST, db=TESTDB)
db_name = "test_trans1_%s" % filename # new namespace!
db = server.new_database(db_name)
count = db.load(original_records)
self.assertEqual(count, len(original_records))
server.commit()
# Now read them back...
biosql_records = [db.lookup(name=rec.name)
for rec in original_records]
# And check they agree
self.assertTrue(compare_records(original_records, biosql_records))
# Now write to a second name space...
db_name = "test_trans2_%s" % filename # new namespace!
db = server.new_database(db_name)
count = db.load(biosql_records)
self.assertEqual(count, len(original_records))
# Now read them back again,
biosql_records2 = [db.lookup(name=rec.name)
for rec in original_records]
# And check they also agree
self.assertTrue(compare_records(original_records, biosql_records2))
# Done
server.close()
def tearDown(self):
destroy_database()
class InDepthLoadTest(unittest.TestCase):
"""Make sure we are loading and retreiving in a semi-lossless fashion."""
def setUp(self):
gb_file = os.path.join(os.getcwd(), "GenBank", "cor6_6.gb")
load_database(gb_file)
self.server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER, passwd=DBPASSWD,
host=DBHOST, db=TESTDB)
self.db = self.server["biosql-test"]
def tearDown(self):
self.server.close()
destroy_database()
del self.db
del self.server
def test_transfer(self):
"""Make sure can load record into another namespace."""
# Should be in database already...
db_record = self.db.lookup(accession="X55053")
# Make a new namespace
db2 = self.server.new_database("biosql-test-alt")
# Should be able to load this DBSeqRecord there...
count = db2.load([db_record])
self.assertEqual(count, 1)
def test_reload(self):
"""Make sure can't reimport existing records."""
gb_file = os.path.join(os.getcwd(), "GenBank", "cor6_6.gb")
gb_handle = open(gb_file, "r")
record = next(SeqIO.parse(gb_handle, "gb"))
gb_handle.close()
# Should be in database already...
db_record = self.db.lookup(accession="X55053")
self.assertEqual(db_record.id, record.id)
self.assertEqual(db_record.name, record.name)
self.assertEqual(db_record.description, record.description)
self.assertEqual(str(db_record.seq), str(record.seq))
# Good... now try reloading it!
try:
count = self.db.load([record])
except Exception as err:
# Good!
self.assertTrue(err.__class__.__name__ in ["IntegrityError",
"AttributeError"],
err.__class__.__name__)
return
raise Exception("Should have failed! Loaded %i records" % count)
def test_record_loading(self):
"""Make sure all records are correctly loaded."""
test_record = self.db.lookup(accession="X55053")
self.assertEqual(test_record.name, "ATCOR66M")
self.assertEqual(test_record.id, "X55053.1")
self.assertEqual(test_record.description, "A.thaliana cor6.6 mRNA")
self.assertTrue(isinstance(test_record.seq.alphabet, Alphabet.DNAAlphabet))
self.assertEqual(str(test_record.seq[:10]), 'AACAAAACAC')
test_record = self.db.lookup(accession="X62281")
self.assertEqual(test_record.name, "ATKIN2")
self.assertEqual(test_record.id, "X62281.1")
self.assertEqual(test_record.description, "A.thaliana kin2 gene")
self.assertTrue(isinstance(test_record.seq.alphabet, Alphabet.DNAAlphabet))
self.assertEqual(str(test_record.seq[:10]), 'ATTTGGCCTA')
def test_seq_feature(self):
"""In depth check that SeqFeatures are transmitted through the db."""
test_record = self.db.lookup(accession="AJ237582")
features = test_record.features
self.assertEqual(len(features), 7)
# test single locations
test_feature = features[0]
self.assertEqual(test_feature.type, "source")
self.assertEqual(str(test_feature.location), "[0:206](+)")
self.assertEqual(len(test_feature.qualifiers), 3)
self.assertEqual(test_feature.qualifiers["country"],
["Russia:Bashkortostan"])
self.assertEqual(test_feature.qualifiers["organism"],
["Armoracia rusticana"])
self.assertEqual(test_feature.qualifiers["db_xref"], ["taxon:3704"])
# test split locations
test_feature = features[4]
self.assertEqual(test_feature.type, "CDS")
self.assertEqual(str(test_feature.location), "join{[0:48](+), [142:206](+)}")
self.assertEqual(len(test_feature.location.parts), 2)
self.assertEqual(str(test_feature.location.parts[0]), "[0:48](+)")
self.assertEqual(str(test_feature.location.parts[1]), "[142:206](+)")
self.assertEqual(test_feature.location.operator, "join")
self.assertEqual(len(test_feature.qualifiers), 6)
self.assertEqual(test_feature.qualifiers["gene"], ["csp14"])
self.assertEqual(test_feature.qualifiers["codon_start"], ["2"])
self.assertEqual(test_feature.qualifiers["product"],
["cold shock protein"])
self.assertEqual(test_feature.qualifiers["protein_id"], ["CAB39890.1"])
self.assertEqual(test_feature.qualifiers["db_xref"], ["GI:4538893"])
self.assertEqual(test_feature.qualifiers["translation"],
["DKAKDAAAAAGASAQQAGKNISDAAAGGVNFVKEKTG"])
# test passing strand information
# XXX We should be testing complement as well
test_record = self.db.lookup(accession="AJ237582")
test_feature = test_record.features[4] # DNA, no complement
self.assertEqual(test_feature.strand, 1)
for loc in test_feature.location.parts:
self.assertEqual(loc.strand, 1)
test_record = self.db.lookup(accession="X55053")
test_feature = test_record.features[0]
# mRNA, so really cDNA, so the strand should be 1 (not complemented)
self.assertEqual(test_feature.strand, 1)
#####################################################################
class AutoSeqIOTests(unittest.TestCase):
"""Test SeqIO and BioSQL together."""
server = None
db = None
@classmethod
def setUpClass(cls):
# Create and reuse on database for all tests in this class
TESTDB = create_database()
def setUp(self):
"""Connect to the database."""
db_name = "biosql-test-seqio"
server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER,
passwd=DBPASSWD,
host=DBHOST, db=TESTDB)
self.server = server
if db_name not in server:
self.db = server.new_database(db_name)
server.commit()
self.db = self.server[db_name]
def tearDown(self):
if self.db:
del self.db
if self.server:
self.server.close()
del self.server
def check(self, t_format, t_filename, t_count=1):
db = self.db
iterator = SeqIO.parse(t_filename, t_format)
count = db.load(iterator)
assert count == t_count
self.server.commit()
iterator = SeqIO.parse(t_filename, t_format)
for record in iterator:
# print(" - %s, %s" % (checksum_summary(record), record.id))
key = record.name
# print(" - Retrieving by name/display_id '%s'," % key)
db_rec = db.lookup(name=key)
compare_record(record, db_rec)
db_rec = db.lookup(display_id=key)
compare_record(record, db_rec)
key = record.id
if key.count(".") == 1 and key.split(".")[1].isdigit():
# print(" - Retrieving by version '%s'," % key)
db_rec = db.lookup(version=key)
compare_record(record, db_rec)
if "accessions" in record.annotations:
# Only expect FIRST accession to work!
key = record.annotations["accessions"][0]
assert key, "Blank accession in annotation %s" % repr(record.annotations)
if key != record.id:
# print(" - Retrieving by accession '%s'," % key)
db_rec = db.lookup(accession=key)
compare_record(record, db_rec)
if "gi" in record.annotations:
key = record.annotations['gi']
if key != record.id:
# print(" - Retrieving by GI '%s'," % key)
db_rec = db.lookup(primary_id=key)
compare_record(record, db_rec)
def test_SeqIO_loading(self):
self.check('fasta', 'Fasta/lupine.nu')
self.check('fasta', 'Fasta/elderberry.nu')
self.check('fasta', 'Fasta/phlox.nu')
self.check('fasta', 'Fasta/centaurea.nu')
self.check('fasta', 'Fasta/wisteria.nu')
self.check('fasta', 'Fasta/sweetpea.nu')
self.check('fasta', 'Fasta/lavender.nu')
self.check('fasta', 'Fasta/aster.pro')
self.check('fasta', 'Fasta/loveliesbleeding.pro')
self.check('fasta', 'Fasta/rose.pro')
self.check('fasta', 'Fasta/rosemary.pro')
self.check('fasta', 'Fasta/f001')
self.check('fasta', 'Fasta/f002', 3)
self.check('fasta', 'Fasta/fa01', 2)
self.check('fasta', 'GFF/NC_001802.fna')
self.check('fasta', 'GFF/multi.fna', 3)
self.check('fasta', 'Registry/seqs.fasta', 2)
self.check('swiss', 'SwissProt/sp001')
self.check('swiss', 'SwissProt/sp002')
self.check('swiss', 'SwissProt/sp003')
self.check('swiss', 'SwissProt/sp004')
self.check('swiss', 'SwissProt/sp005')
self.check('swiss', 'SwissProt/sp006')
self.check('swiss', 'SwissProt/sp007')
self.check('swiss', 'SwissProt/sp008')
self.check('swiss', 'SwissProt/sp009')
self.check('swiss', 'SwissProt/sp010')
self.check('swiss', 'SwissProt/sp011')
self.check('swiss', 'SwissProt/sp012')
self.check('swiss', 'SwissProt/sp013')
self.check('swiss', 'SwissProt/sp014')
self.check('swiss', 'SwissProt/sp015')
self.check('swiss', 'SwissProt/sp016')
self.check('swiss', 'Registry/EDD_RAT.dat')
self.check('genbank', 'GenBank/noref.gb')
self.check('genbank', 'GenBank/cor6_6.gb', 6)
self.check('genbank', 'GenBank/iro.gb')
self.check('genbank', 'GenBank/pri1.gb')
self.check('genbank', 'GenBank/arab1.gb')
with warnings.catch_warnings():
# BiopythonWarning: order location operators are not fully
# supported
warnings.simplefilter("ignore", BiopythonWarning)
self.check('genbank', 'GenBank/protein_refseq2.gb')
self.check('genbank', 'GenBank/extra_keywords.gb')
self.check('genbank', 'GenBank/one_of.gb')
self.check('genbank', 'GenBank/NT_019265.gb')
self.check('genbank', 'GenBank/origin_line.gb')
self.check('genbank', 'GenBank/blank_seq.gb')
with warnings.catch_warnings():
# BiopythonWarning: bond location operators are not fully supported
warnings.simplefilter("ignore", BiopythonWarning)
self.check('genbank', 'GenBank/dbsource_wrap.gb')
# BiopythonWarning: order location operators are not fully
# supported
self.check('genbank', 'GenBank/NC_005816.gb')
self.check('genbank', 'GenBank/gbvrl1_start.seq', 3)
self.check('genbank', 'GFF/NC_001422.gbk')
self.check('embl', 'EMBL/TRBG361.embl')
self.check('embl', 'EMBL/DD231055_edited.embl')
self.check('embl', 'EMBL/SC10H5.embl')
self.check('embl', 'EMBL/U87107.embl')
self.assertEqual(len(self.db), 66)
class SwissProtUnknownPositionTest(unittest.TestCase):
"""Handle SwissProt unknown position by setting value to null in database."""
def setUp(self):
# drop any old database and create a new one:
TESTDB = create_database()
# connect to new database:
self.server = BioSeqDatabase.open_database(driver=DBDRIVER,
user=DBUSER, passwd=DBPASSWD,
host=DBHOST, db=TESTDB)
# Create new namespace within new empty database:
self.db = self.server.new_database("biosql-test")
def tearDown(self):
self.server.rollback()
self.server.close()
destroy_database()
del self.db
del self.server
def test_ambiguous_location(self):
"""Loaded uniprot-xml with ambiguous location in BioSQL."""
id = 'P97881'
seqiter = SeqIO.parse("SwissProt/%s.xml" % id, "uniprot-xml")
self.assertTrue(self.db.load(seqiter) == 1)
dbrecord = self.db.lookup(primary_id=id)
for feature in dbrecord.features:
if feature.type == 'signal peptide':
self.assertTrue(isinstance(feature.location.end, UnknownPosition))
elif feature.type == 'chain':
self.assertTrue(isinstance(feature.location.start, UnknownPosition))
else:
self.assertTrue(isinstance(feature.location.start, ExactPosition))