def test_guess_seq_type(self):
'It guesses if the sequence is nucleotide or protein'
fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
assert guess_seq_type(open(fpath)) == 'nucl'
fpath = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
assert guess_seq_type(open(fpath)) == 'nucl'
def test_guess_seq_type(self):
'It guesses if the sequence is nucleotide or protein'
fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
assert guess_seq_type(open(fpath)) == 'nucl'
fpath = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
assert guess_seq_type(open(fpath)) == 'nucl'
def get_or_create_blastdb(blastdb_or_path, dbtype=None, directory=None):
'''it returns a blast database.
If it does not exists it creates and if you give it a directory it will
create it in that directory if it does not exist yet
'''
seq_fpath = _get_abs_blastdb_path(blastdb_or_path, dbtype)
if directory:
dbname = os.path.basename(seq_fpath)
dbpath = os.path.join(directory, dbname)
else:
dbpath = seq_fpath
if not _blastdb_exists(dbpath, dbtype=dbtype):
if not os.path.exists(seq_fpath):
msg = 'An input sequence is required to create a blastdb'
raise RuntimeError(msg)
if seq_fpath != dbpath:
seqio([open(seq_fpath)],
open(dbpath, 'w'),
out_format='fasta',
copy_if_same_format=False)
if dbtype is None:
dbtype = guess_seq_type(open(dbpath))
_makeblastdb_plus(dbpath, dbtype)
return dbpath
def get_or_create_blastdb(blastdb_or_path, dbtype=None, directory=None):
'''it returns a blast database.
If it does not exists it creates and if you give it a directory it will
create it in that directory if it does not exist yet
'''
seq_fpath = _get_abs_blastdb_path(blastdb_or_path, dbtype)
if directory:
dbname = os.path.basename(seq_fpath)
dbpath = os.path.join(directory, dbname)
else:
dbpath = seq_fpath
if not _blastdb_exists(dbpath, dbtype=dbtype):
if not os.path.exists(seq_fpath):
msg = 'An input sequence is required to create a blastdb'
raise RuntimeError(msg)
if seq_fpath != dbpath:
seqio([open(seq_fpath)], open(dbpath, 'w'), out_format='fasta',
copy_if_same_format=False)
if dbtype is None:
dbtype = guess_seq_type(open(dbpath))
_makeblastdb_plus(dbpath, dbtype)
return dbpath
def test_guess_seq_type():
'It checks that we can guess the type of the seqs in a file'
fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
guess_seq_type(open(fpath))
def test_guess_seq_type():
'It checks that we can guess the type of the seqs in a file'
fpath = os.path.join(TEST_DATA_DIR, 'arabidopsis_genes')
guess_seq_type(open(fpath))
