def __init__(self,
seq_repo_path=None,
regions_preload=None,
preload_pos_margin=500,
assembly_name=None):
'''
:param seq_repo_path: Path to local seqrepo directory. If None, read HGVS_SEQREPO_DIR environment variable
:param regions_preload: Iterable[ChrInterval], optionally preload these genomic regions
:param preload_pos_margin: adding margin at the end of a preloaded genome
in order to have data to verify structural variants across the end of a gene
'''
if not seq_repo_path:
seq_repo_path = os.environ.get("HGVS_SEQREPO_DIR")
if seq_repo_path:
seq_repo = SeqRepo(seq_repo_path)
self.seq_repo_fetcher = seq_repo.fetch
else:
logging.warn("Using remote sequence provider.")
self.seq_repo_fetcher = seqfetcher.fetch_seq
self.assembly_name = assembly_name
if not self.assembly_name:
self.assembly_name = self.DEFAULT_ASSY_NAME
self.assy_map = assemblies.make_name_ac_map(self.assembly_name)
self.preloaded_regions = {}
if regions_preload:
self.preloaded_regions = build_interval_trees_by_chr(
regions_preload,
lambda c, s, e: self._fetch_seq(c, s, e + preload_pos_margin))
def __init__(self):
# If HGVS_SEQREPO_DIR is defined, we use seqrepo for *all* sequences.
# If HGVS_SEQREPO_URL is defined, use instance of seqrepo-rest-service for *all* sequences.
# (see https://github.com/biocommons/seqrepo-rest-service for more info)
# Otherwise, we fall back to remote sequence fetching
seqrepo_dir = os.environ.get("HGVS_SEQREPO_DIR")
seqrepo_url = os.environ.get("HGVS_SEQREPO_URL")
if seqrepo_dir:
from biocommons.seqrepo import SeqRepo
self.sr = SeqRepo(seqrepo_dir)
def _fetch_seq_seqrepo(ac, start_i=None, end_i=None):
return self.sr.fetch(ac, start_i, end_i)
self.fetcher = _fetch_seq_seqrepo
self.source = "SeqRepo ({})".format(seqrepo_dir)
elif seqrepo_url:
from biocommons.seqrepo.dataproxy import SeqRepoRESTDataProxy
self.sr = SeqRepoRESTDataProxy(seqrepo_url)
self.fetcher = lambda ac, start_i=None, end_i=None: self.sr.get_sequence(
ac, start_i, end_i)
self.source = f"SeqRepo REST ({seqrepo_url})"
else:
self.sr = None
self.fetcher = bioutils.seqfetcher.fetch_seq
self.source = "bioutils.seqfetcher (network fetching)"
_logger.info("Fetching sequences with " + self.source)
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_seqrepo_dir_not_exist(tmpdir_factory):
"""Ensure that exception is raised for non-existent seqrepo directory"""
dir = str(tmpdir_factory.mktemp('seqrepo')) + "-IDONTEXIST"
with pytest.raises(OSError) as ex:
SeqRepo(dir, writeable=False)
assert "Unable to open SeqRepo directory" in str(ex.value)
def get_seqrepo(self, seqrepo_dir) -> SeqRepo:
"""Return SeqRepo instance if seqrepo_dir exists.
:param Path seqrepo_dir: Path to seqrepo directory
:return: SeqRepo instance
"""
if not Path(seqrepo_dir).exists():
raise NotADirectoryError(f"Could not find {seqrepo_dir}")
return SeqRepo(seqrepo_dir)
def __init__(self):
# If HGVS_SEQREPO_DIR is defined, we use seqrepo for *all* sequences
# Otherwise, we fall back to remote sequence fetching
seqrepo_dir = os.environ.get("HGVS_SEQREPO_DIR")
if seqrepo_dir:
from biocommons.seqrepo import SeqRepo
self.sr = SeqRepo(seqrepo_dir)
def _fetch_seq_seqrepo(ac, start_i=None, end_i=None):
return self.sr.fetch(ac, start_i, end_i)
self.fetcher = _fetch_seq_seqrepo
self.source = "SeqRepo ({})".format(seqrepo_dir)
else:
self.sr = None
self.fetcher = bioutils.seqfetcher.fetch_seq
self.source = "bioutils.seqfetcher (network fetching)"
_logger.info("Fetching sequences with " + self.source)
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 __init__(self):
# If HGVS_SEQREPO_DIR is defined, we use seqrepo for *all* sequences
# Otherwise, we fall back to remote sequence fetching
seqrepo_dir = os.environ.get("HGVS_SEQREPO_DIR")
if seqrepo_dir:
from biocommons.seqrepo import SeqRepo
sr = SeqRepo(seqrepo_dir)
def _fetch_seq_seqrepo(ac, start_i=None, end_i=None):
return sr.fetch(ac, start_i, end_i)
self.fetcher = _fetch_seq_seqrepo
logger.info(
"Using SeqRepo({}) sequence fetching".format(seqrepo_dir))
else:
self.fetcher = bioutils.seqfetcher.fetch_seq
logger.info("Using remote sequence fetching")
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"
class SeqFetcher(object):
"""This class is intended primarily as a mixin for HGVS data providers
that doen't otherwise have access to sequence data. It uses the
fetch_seq() function in this module to fetch sequences from
several sources; see that function for details.
>> sf = SeqFetcher()
>> sf.fetch_seq('NP_056374.2',0,10)
'MESRETLSSS'
"""
def __init__(self):
# If HGVS_SEQREPO_DIR is defined, we use seqrepo for *all* sequences
# Otherwise, we fall back to remote sequence fetching
seqrepo_dir = os.environ.get("HGVS_SEQREPO_DIR")
if seqrepo_dir:
from biocommons.seqrepo import SeqRepo
self.sr = SeqRepo(seqrepo_dir)
def _fetch_seq_seqrepo(ac, start_i=None, end_i=None):
return self.sr.fetch(ac, start_i, end_i)
self.fetcher = _fetch_seq_seqrepo
self.source = "SeqRepo ({})".format(seqrepo_dir)
else:
self.sr = None
self.fetcher = bioutils.seqfetcher.fetch_seq
self.source = "bioutils.seqfetcher (network fetching)"
_logger.info("Fetching sequences with " + self.source)
def fetch_seq(self, ac, start_i=None, end_i=None):
try:
return self.fetcher(ac, start_i, end_i)
except Exception as ex:
raise HGVSDataNotAvailableError(
"Failed to fetch {ac} from {self.source} ({ex})".format(
ac=ac, ex=ex, self=self))
def seqrepo_keepcase(tmpdir_factory):
dir = str(tmpdir_factory.mktemp('seqrepo'))
return SeqRepo(dir, upcase=False, writeable=True)
def seqrepo_ro(tmpdir_factory):
dir = str(tmpdir_factory.mktemp('seqrepo'))
sr = SeqRepo(dir, writeable=True)
del sr # close it
return SeqRepo(dir)
def _get_seqrepo(cf):
sr_dir = cf.get("sequences", "seqrepo")
sr = SeqRepo(root_dir=sr_dir, translate_ncbi_namespace=True)
logger.info("Opened {sr}".format(sr=sr))
return sr
def create_text(self, defn):
vo = models.Text(definition=defn)
vo._id = ga4gh_identify(vo)
return vo
if __name__ == "__main__":
import os
from biocommons.seqrepo import SeqRepo
from ga4gh.vrs.dataproxy import SeqRepoRESTDataProxy, SeqRepoDataProxy
if "SEQREPO_DIR" in os.environ:
seqrepo_dir = os.environ.get("SEQREPO_DIR",
"/usr/local/share/seqrepo/latest")
data_proxy = SeqRepoDataProxy(SeqRepo(root_dir=seqrepo_dir))
else:
seqrepo_url = os.environ.get(
"GA4GH_VRS_DATAPROXY_URI",
"https://services.genomicmedlab.org/seqrepo")
data_proxy = SeqRepoRESTDataProxy(base_url=seqrepo_url)
object_store = {}
av = AnyVar(data_proxy=data_proxy, object_store=object_store)
v = av.translate_allele("NM_000551.3:c.1A>T", fmt="hgvs")
vid = av.put_object(v)
v2 = av.get_object(vid, deref=True)
assert v == v2 # roundtrip test
def search():
from biocommons.seqrepo import SeqRepo
sr = SeqRepo("/usr/local/share/seqrepo/latest")
#return [sr[key] for key in sorted(sr.keys())]
return sr["NC_000001.11"][780000:780020
def _get_seqrepo(cf):
sr_dir = cf.get("sequences", "seqrepo")
sr = SeqRepo(root_dir=sr_dir)
logger.info("Opened sequence directory " + sr_dir)
return sr
def seqrepo(tmpdir_factory):
dir = str(tmpdir_factory.mktemp('seqrepo'))
return SeqRepo(dir, writeable=True)
def _get_seqrepo(cf):
sr_dir = cf.get("sequences", "seqrepo")
sr = SeqRepo(root_dir=sr_dir)
logger.info("Opened {sr}".format(sr=sr))
return sr
