Chris,
I've been rooting around in seqdb again, trying to understand exactly
how to make my own on-disk sequence database implementation (as a
prelude to making an implementation available based on Alex's code for
large short-read dbs).
I thought I'd start by making my own in-memory seq db class; here's what
I've got so far:
---
class MemSequence(SequenceBase):
def _init_subclass(cls, db, **kwargs):
cls.db = db
db.seqInfoDict = kwargs['theDict']
_init_subclass = classmethod(_init_subclass)
def __init__(self, db, id):
self.id = id
SequenceBase.__init__(self)
self.seq = db.seqInfoDict[id]
class MemSequenceDB(SequenceDB):
itemClass = MemSequence
---
You can use this by taking a dictionary of sequences and passing it in
as the 'theDict' argument:
---
d = dict(a='ATCG', b='ATGGCAT')
memdb = MemSequenceDB(theDict=d)
---
In essence, all that's happening is that the dictionary 'd' becomes
db.seqInfoDict; the rest is just machinery surrounding that.
So, my question to you is, is this a reasonable start? I realize that
MemSequenceDB
- isn't pickleable; not sure exactly what I'd need to do to implement
that;
- doesn't do any caching or anything clever with strslice;
So, my next step is to provide a simple dict-like interface to Alexs
code that can then replace 'd'. Anything else I need to note in order
to proceed with linking this to an actual on-disk file of sequences?
thanks,
--titus
--
C. Titus Brown, [email protected]
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