[pygr-notify] [pygr commit] r104 - wiki

[codesite-noreply at google.com]

Author: jqian.ubc
Date: Wed Sep 10 20:41:11 2008
New Revision: 104

Modified:
    wiki/PygrOnEnsembl.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/PygrOnEnsembl.wiki
==============================================================================
--- wiki/PygrOnEnsembl.wiki	(original)
+++ wiki/PygrOnEnsembl.wiki	Wed Sep 10 20:41:11 2008
@@ -67,25 +67,25 @@

  *1.* the datamodel module (datamodel.py):

-*-* a generic datamodel (BaseModel) class (super class).  It is a subclass  
of the Pygr's sqlgraph.TupleO
+*-* a generic datamodel (BaseModel) class (super class).  It is a subclass  
of the Pygr's sqlgraph.TupleO.

  *-* specialized datamodel classes (subclasses of BaseModel).  Each  
subclass represents a biological entity, or an Ensembl row/item object.

-*-* a generic Feature class.  It represents a generic Ensembl feature.  An  
Ensembl feature refers to an object that has the attributes of  
seq_region_id, seq_region_start, seq_region_end and seq_region_strand.  The  
get_sequence() method is implemented using Pygr's seqdb.AnnotationDB
+*-* a generic Feature class.  It represents a generic Ensembl feature.  An  
Ensembl feature refers to an object that has the attributes of  
seq_region_id, seq_region_start, seq_region_end and seq_region_strand.  The  
get_sequence() method is implemented using Pygr's seqdb.AnnotationDB.

-*-* specialized feature classes (subclasses of Feature).  The schema  
between features is implemented using Pygr's sqlgraph.SQLGraph
+*-* specialized feature classes (subclasses of Feature).  The schema  
between features is implemented using Pygr's sqlgraph.SQLGraph.

  *2.* the adaptor module (adaptor.py):

  *-* a Registry class: provides a connection to the ensembl SQL server

-*-* specialized adaptor classes (subclasses of Pygr's sqlgraph.SQLTable  
class): provides access to a specific sql table in an ensembl core database.
+*-* specialized adaptor classes (subclasses of Pygr's sqlgraph.SQLTable  
class): provides access to a specific sql table in an ensembl core database

  *-* private module methods: provide automatic saving of the Ensembl  
database schema to pygr.Data

  *3.* the featuremapping module (featuremapping.py): provides mapping  
between ensembl features

-*4.* the supporting module (seqregion.py): provides mapping between a  
sequence slice and the set of Ensembl features in the slice.
+*4.* the supporting module (seqregion.py): provides mapping between a  
sequence slice and the set of Ensembl features in the slice

  *Design Pattern*

@@ -106,6 +106,7 @@
  `coreDBAdaptor =  
serverRegistry.get_DBAdaptor('homo_sapiens', 'core', '47_36i')`

  Retrieve a sequence object:
+

  `coreDBAdaptor.fetch_slice_by_seqregion(coordSystemName, seqregionName)`

@@ -137,6 +138,7 @@
  An ensembl feature refers to an object that has the attributes of  
seq_region_id, seq_region_start, seq_region_end and seq_region_strand.

  Retrieve the sequence of an ensembl feature:
+
  `get_sequence()`

  e.g.