[pygr-notify] [pygr commit] r102 - wiki

[codesite-noreply at google.com]

Author: jqian.ubc
Date: Wed Sep 10 20:19:30 2008
New Revision: 102

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 20:19:30 2008
@@ -66,15 +66,22 @@
  *Framework*

  *1.* the datamodel module (datamodel.py):
-- 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
-- specialized feature classes (subclasses of Feature).  The schema between  
features is implemented using Pygr's sqlgraph.SQLGraph
+
+*-* 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
+
+*-* 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.
-- private module methods: provide automatic saving of the Ensembl database  
schema to pygr.Data
+
+*-* 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.
+
+*-* 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

@@ -102,10 +109,12 @@

  `coreDBAdaptor.fetch_slice_by_seqregion(coordSystemName, seqregionName)`

--coordSystemName: 'chromosome' or 'contig'
--seqreionName: a chromosome name, such as '1'
-	               or a contig name, such as 'AADC01095577.1.1.41877'
--optional arguments for this method: start, end, strand
+- coordSystemName: 'chromosome' or 'contig'
+
+- seqreionName: a chromosome name, such as '1'
+  or a contig name, such as 'AADC01095577.1.1.41877'
+
+- optional arguments for this method: start, end, strand

  Create access to any table in an ensembl core database:

@@ -145,31 +154,31 @@
  e.g.
  `transcriptAdaptor.fetch_all_by_slice(slice)` will retrieve all the  
transcripts in the give slice.

-Retrieve the stable_id, created_date, modified_date or the version for a  
gene/transcript/translation/exon
+Retrieve the stable_id, created_date, modified_date or the version for a  
gene/transcript/translation/exon:

  e.g.
  `gene.get_stable_id()` will return the ensembl stable_id for the given gene

  Obtain a gene object:

-`transcript.get_gene()`
+`transcript.get_gene()`,
  `geneAdaptor.fetch_by_stable_id(geneStableID)`

  Obtain transcript objects:

-`gene.get_transcripts()`
-`exon.get_all_transcripts()`
-`translation.get_transcript()`
+`gene.get_transcripts()`,
+`exon.get_all_transcripts()`,
+`translation.get_transcript()`,
  `transcriptAdaptor.fetch_by_stable_id(transcriptStableID)`

  Obtain exon objects:

-`transcript.get_all_exons()`
+`transcript.get_all_exons()`,
  `exonAdaptor.fetch_by_stable_id(exonStableID)`

  Obtain a translation object:

-`transcript.get_translation()`
+`transcript.get_translation()`,
  `translationAdaptor.fetch_by_stable_id(translationStableID)`

  Obtain a spliced sequence object: