def make_seqrepo(writeable):
sr = SeqRepo("/tmp/sr", writeable=True)
sr.store("SMELLASSWEET", [{"namespace": "en", "alias": "rose"}, {"namespace": "fr", "alias": "rose"}])
if writeable is False:
del sr
sr = SeqRepo("/tmp/sr", writeable=writeable)
print("pid {pid} created {sr}".format(pid=os.getpid(), sr=sr))
return sr
def test_refseq_translation(tmpdir_factory):
dir = str(tmpdir_factory.mktemp('seqrepo'))
seqrepo = SeqRepo(dir, writeable=True)
seqrepo.store("NCBISEQUENCE", [{"namespace": "NCBI", "alias": "ncbiac"}])
seqrepo.commit()
del seqrepo
seqrepo = SeqRepo(dir, writeable=False, translate_ncbi_namespace=False)
aliases = list(seqrepo.aliases.find_aliases(alias="ncbiac"))
assert len(aliases) == 1
assert aliases[0]["namespace"] == "NCBI"
seqrepo = SeqRepo(dir, writeable=False, translate_ncbi_namespace=True)
aliases = list(seqrepo.aliases.find_aliases(alias="ncbiac"))
assert len(aliases) == 1
assert aliases[0]["namespace"] == "RefSeq"
def test_refseq_translation(tmpdir_factory):
dir = str(tmpdir_factory.mktemp('seqrepo'))
seqrepo = SeqRepo(dir, writeable=True)
seqrepo.store("NCBISEQUENCE", [{"namespace": "NCBI", "alias": "ncbiac"}])
seqrepo.commit()
del seqrepo
seqrepo = SeqRepo(dir, writeable=False, translate_ncbi_namespace=False)
aliases = list(seqrepo.aliases.find_aliases(alias="ncbiac"))
assert len(aliases) == 1
assert aliases[0]["namespace"] == "NCBI"
seqrepo = SeqRepo(dir, writeable=False, translate_ncbi_namespace=True)
aliases = list(seqrepo.aliases.find_aliases(alias="ncbiac"))
assert len(aliases) == 1
assert aliases[0]["namespace"] == "RefSeq"