def test_blastdb():
'It creates a blast database.'
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
db_dir = TemporaryDir(prefix='blast_dbs_')
try:
db_path1 = get_or_create_blastdb(seq_fpath, directory=db_dir.name,
dbtype='nucl')
db_path = os.path.join(db_dir.name, db_name)
assert 'CATAGGGTCACCAATGGC' in open(db_path1).read(100)
assert db_path1 == db_path
assert os.path.exists(db_path)
index_fpath = os.path.join(db_dir.name, db_name + '.nsq')
assert os.path.exists(index_fpath)
finally:
db_dir.close()
def test_blast_search(self):
'It does a blast search'
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
db_dir = TemporaryDir(prefix='blast_dbs_')
try:
db_fpath = get_or_create_blastdb(seq_fpath, directory=db_dir.name,
dbtype='nucl')
query_fhand = NamedTemporaryFile()
query_fhand.write(open(seq_fpath).read(200))
query_fhand.flush()
out_fhand = NamedTemporaryFile()
do_blast(seq_fpath, db_fpath, program='blastn',
out_fpath=out_fhand.name)
assert '</BlastOutput>' in open(out_fhand.name).read()
finally:
db_dir.close()
def test_blastdb():
'It creates a blast database.'
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
db_dir = TemporaryDir(prefix='blast_dbs_')
try:
db_path1 = get_or_create_blastdb(seq_fpath,
directory=db_dir.name,
dbtype='nucl')
db_path = os.path.join(db_dir.name, db_name)
assert 'CATAGGGTCACCAATGGC' in open(db_path1).read(100)
assert db_path1 == db_path
assert os.path.exists(db_path)
index_fpath = os.path.join(db_dir.name, db_name + '.nsq')
assert os.path.exists(index_fpath)
finally:
db_dir.close()
def test_blast_search(self):
'It does a blast search'
db_name = 'arabidopsis_genes'
seq_fpath = os.path.join(TEST_DATA_DIR, db_name)
db_dir = TemporaryDir(prefix='blast_dbs_')
try:
db_fpath = get_or_create_blastdb(seq_fpath,
directory=db_dir.name,
dbtype='nucl')
query_fhand = NamedTemporaryFile()
query_fhand.write(open(seq_fpath).read(200))
query_fhand.flush()
out_fhand = NamedTemporaryFile()
do_blast(seq_fpath,
db_fpath,
program='blastn',
out_fpath=out_fhand.name)
assert '</BlastOutput>' in open(out_fhand.name).read()
finally:
db_dir.close()
def test_get_or_create_blastdb():
blastdb = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
directory = TemporaryDir()
assert not _blastdb_exists(blastdb, NUCL)
get_or_create_blastdb(blastdb, NUCL, directory.name)
new_blast_path = os.path.join(directory.name,
os.path.basename(blastdb))
assert _blastdb_exists(new_blast_path, NUCL)
get_or_create_blastdb(blastdb, NUCL, directory.name)
assert _blastdb_exists(new_blast_path, NUCL)
directory.close()
# already exists
blastdb = os.path.join(TEST_DATA_DIR, 'blastdbs', 'arabidopsis_genes')
assert _blastdb_exists(blastdb, NUCL)
get_or_create_blastdb(blastdb, NUCL)
assert _blastdb_exists(blastdb, NUCL)
def test_get_or_create_blastdb():
blastdb = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
directory = TemporaryDir()
assert not _blastdb_exists(blastdb, NUCL)
get_or_create_blastdb(blastdb, NUCL, directory.name)
new_blast_path = os.path.join(directory.name,
os.path.basename(blastdb))
assert _blastdb_exists(new_blast_path, NUCL)
get_or_create_blastdb(blastdb, NUCL, directory.name)
assert _blastdb_exists(new_blast_path, NUCL)
directory.close()
# already exists
blastdb = os.path.join(TEST_DATA_DIR, 'blastdbs', 'arabidopsis_genes')
assert _blastdb_exists(blastdb, NUCL)
get_or_create_blastdb(blastdb, NUCL)
assert _blastdb_exists(blastdb, NUCL)