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Package refget Documentation

Class RefGetClient

def __init__(self, api_url_base=None, database={}, schemas=[], schemas_str=[], henges=None, checksum_function=<function md5 at 0x7f27a640c180>, suppress_connect=True)

A user interface to insert and retrieve decomposable recursive unique identifiers (DRUIDs).


  • database (dict): Dict-like lookup database with sequences and hashes.
  • schemas (dict): One or more jsonschema schemas describing thedata types stored by this Henge
  • checksum_function (function(str) -> str): Default function to handle the digest of theserialized items stored in this henge.
def get_service_info(self)
def item_types(self)

A list of item types handled by this Henge instance

def load_fasta(self, fa_file, lengths_only=False)

Calculates checksums and loads each sequence in a fasta file into the database.

def load_seq(self, seq)
def load_sequence_dict(self, seqset)

Convert a 'seqset', which is a dict with names as sequence names and values as sequences, into the 'asdlist' required for henge insert.

def meta(self, digest)
def refget(self, digest, start=None, end=None)
def refget_remote(self, digest, start=None, end=None)
def service_info(self)

Version Information: refget v0.2.0, generated by lucidoc v0.4.4