Python SeqRepo.store Beispiele

Beispiel #1

Datei: threading-verification.py Projekt: ypchan/biocommons.seqrepo

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

Beispiel #2

Datei: test_seqrepo.py Projekt: ypchan/biocommons.seqrepo

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"

Beispiel #3

Datei: test_seqrepo.py Projekt: biocommons/seqrepo

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"