def get_Seqs_by_acc(self, name):
"""Gets a *list* of Bio::Seq objects by accession number
Example: seqs = db.get_Seq_by_acc('X77802')
"""
seqids = self.adaptor.fetch_seqids_by_accession(self.dbid, name)
return [BioSeq.DBSeqRecord(self.adaptor, seqid) for seqid in seqids]
def get_Seq_by_ver(self, name):
"""Gets a Bio::Seq object by version number
Example: seq = db.get_Seq_by_ver('X77802.1')
"""
seqid = self.adaptor.fetch_seqid_by_version(self.dbid, name)
return BioSeq.DBSeqRecord(self.adaptor, seqid)
def get_Seq_by_id(self, name):
"""Gets a Bio::Seq object by its name
Example: seq = db.get_Seq_by_id('ROA1_HUMAN')
"""
seqid = self.adaptor.fetch_seqid_by_display_id(self.dbid, name)
return BioSeq.DBSeqRecord(self.adaptor, seqid)
def get_Seq_by_ver(self, name):
"""Gets a DBSeqRecord object by version number
Example: seq_rec = db.get_Seq_by_ver('X77802.1')
The name of this method is misleading since it returns a DBSeqRecord
rather than a DBSeq ojbect, and presumably was to mirror BioPerl.
"""
seqid = self.adaptor.fetch_seqid_by_version(self.dbid, name)
return BioSeq.DBSeqRecord(self.adaptor, seqid)
def get_Seq_by_id(self, name):
"""Gets a DBSeqRecord object by its name
Example: seq_rec = db.get_Seq_by_id('ROA1_HUMAN')
The name of this method is misleading since it returns a DBSeqRecord
rather than a DBSeq ojbect, and presumably was to mirror BioPerl.
"""
seqid = self.adaptor.fetch_seqid_by_display_id(self.dbid, name)
return BioSeq.DBSeqRecord(self.adaptor, seqid)
def lookup(self, **kwargs):
if len(kwargs) != 1:
raise TypeError("single key/value parameter expected")
k, v = kwargs.items()[0]
if k not in _allowed_lookups:
raise TypeError("lookup() expects one of %s, not %r" % \
(repr(_allowed_lookups.keys())[1:-1], repr(k)))
lookup_name = _allowed_lookups[k]
lookup_func = getattr(self.adaptor, lookup_name)
seqid = lookup_func(self.dbid, v)
return BioSeq.DBSeqRecord(self.adaptor, seqid)
def get_Seqs_by_acc(self, name):
"""Gets a list of DBSeqRecord objects by accession number
Example: seq_recs = db.get_Seq_by_acc('X77802')
The name of this method is misleading since it returns a list of
DBSeqRecord objects rather than a list of DBSeq ojbects, and presumably
was to mirror BioPerl.
"""
seqids = self.adaptor.fetch_seqids_by_accession(self.dbid, name)
return [BioSeq.DBSeqRecord(self.adaptor, seqid) for seqid in seqids]
def __getitem__(self, key):
return BioSeq.DBSeqRecord(self.adaptor, key)