[pygr-notify] [pygr commit] r89 - wiki

[codesite-noreply at google.com]

Author: cjlee112
Date: Mon Aug 11 20:19:27 2008
New Revision: 89

Added:
    wiki/SequenceDBModel.wiki

Log:
Created wiki page through web user interface.

Added: wiki/SequenceDBModel.wiki
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+#summary Concise summary of the Pygr sequence database model.
+
+= Introduction =
+
+We're trying to simplify Pygr's data models for the 0.8 release.  Here  
I'll propose how we might refactor the sequence database model a bit.  My  
main goals:
+  * call the base class SequenceDB.  Put all BLAST support in a subclass.
+  * define a standard, modular API to the actual storage, so no storage  
code is mixed up in the SequenceDB class.  It should be possible to use  
different storage classes with SequenceDB.
+  * let users define / supply any sequence reading function they want.
+  * start using the standard get_bound_subclass() system for handling  
itemClass, the same as in other parts of Pygr.
+
+
+== Proposed SequenceDB model ==
+
+=== What's New ===
+The main change is modularizing the storage access mechanisms into the the  
*seqInfoDict* and `_init_subclass()` classmethod supplied by the  
*itemClass*.
+
+  * *itemClass* attribute: class to use for each top-level sequence  
object.  I propose that all functions for storage access (building and  
searching the index) be part of the itemClass, since it represents the  
storage interface.
+  * *itemSliceClass* attribute: class to use for sequence sub-slice objects
+  * *seqInfoDict* attribute: dictionary interface to sequence information  
from the storage mechanism.  Returns an object with attributes like  
*length*, *title* and possibly others like *offset*.  This is the official  
mechanism for getting some information about what's in the database without  
actually triggering the construction of a sequence object.  This interface  
is needed for things like NLMSA that will need to construct union  
coordinate systems that unify one or more sequence databases.
+  * `__getitem__(seqID)`: get the sequence object with this ID
+  * `__len__()`: get total number of sequences in this database
+  * `__invert__()`: get reverse mapping object (maps sequence obj to its  
ID).
+  * `__contains__(B)`: True if the argument is a sequence in this database
+  * `__iter__()` etc.: all the standard dictionary iterators
+  * `cacheHint(owner, ivalDict)`: save a cache hint dict of  
{id:(start,stop)} associated with owner
+  * `strsliceCache(seq,start,stop)`: get strslice using cache hints, if any
+
+
+== Sequence model ==
+  * *id* attribute: gives the ID of the sequence (primary key within its  
database)
+  * *db* attribute: points to the database object containing this sequence
+  * *orientation*: 1 if forward strand, -1 if negative strand
+  * *path*: the complete sequence object containing this sequence interval
+  * `__getitem__(slice)`: slice this sequence
+  * `__len__()`: get this sequence's length
+  * `__str__()`: get this sequence interval's sequence string
+  * `__neg__()`: get reverse-complement of this sequence interval  
(ValueError if protein)
+  * `__add__(B)`: get union with another sequence interval, i.e. A+B  
covers the interval [A.start,B.stop]. (ValueError if not in the same parent  
sequence).
+  * `__contains__(B)`: True if the argument is a sub-interval of this  
sequence interval
+  * `__mul__(B)`: get intersection with another sequence interval, i.e.  
A*B is the largest interval contained both in A and in B.
+  * `before()`: get the entire interval up to this sequence (adjacent on  
the left)
+  * `after()`: get the entire interval after this sequence (adjacent on  
the right)
+  * `seqtype()`: get type (nucleotide or protein) of this sequence
+=== Additional implementor methods ===
+  * `strslice(start, stop)`: get string corresponding to sequence for  
interval [start,stop].  This is the primary interface to the actual storage.
+  * `_init_subclass(seqReader=None)`: classmethod on the itemClass, that  
initializes connection to the storage, constructing the index if necessary,  
and adds a *seqInfoDict* attribute to the sequence database object.  Should  
accept a seqReader method argument that iterates all the sequences in the  
input file and returns all the IDs and sequences.
+
+