[pygr-notify] [pygr commit] r76 - wiki

[codesite-noreply at google.com]

Author: ramccreary
Date: Sun Jul 13 19:54:25 2008
New Revision: 76

Modified:
   wiki/DataStorageUsingpygr.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/DataStorageUsingpygr.wiki
==============================================================================
--- wiki/DataStorageUsingpygr.wiki	(original)
+++ wiki/DataStorageUsingpygr.wiki	Sun Jul 13 19:54:25 2008
@@ -2,7 +2,7 @@

 = Introduction =

-This article is an in-depth explanation of a script in which a genome 
and the accompanying annotations are stored in multiple ways, including 
a MySQL database and pygr.Data. Storing the data this way enables it to 
be easily manipulated using pygr and prevents potential errors by 
allowing ease of access to the necessary genomic information.
+This article is an in-depth explanation of a script in which a genome 
and the accompanying annotations are manipulated in multiple 
ways,including in a MySQL table, and then stored in pygr.Data, a 
resource database. Storing the data this way enables it to be easily 
manipulated using pygr and prevents potential errors by allowing ease 
of access to the necessary genomic information.


 = Step-By-Step Example =
@@ -161,12 +161,6 @@

             conn.commit()

-
-
-        if n > 1000:
-
-            break
-


 conn.commit()
@@ -217,7 +211,7 @@
 annot_map.build()
 }}}

-Docstrings are then created for the genome, the annotations, and the 
annotation map so they may be stored in pygr.Data. pygr.Data requires 
docstrings to be assigned to every resources stored within, to allow a 
more transparent storage of data and to allow easier access.
+Docstrings are then created for the genome, the annotations, and the 
annotation map so they may be stored in pygr.Data. pygr.Data requires 
docstrings to be assigned to every resources stored within, to allow a 
more descriptive storage of resources and to allow easier access.

  Finally, the genome, the annotation, and the annotation map is stored 
in pygr.Data. Since the annotation map is a schema, its can be stored 
in pygr.Data as a schema. In order to store schema in pygr.Data, the 
relationship between the schema must be defined (Many-To-Many or 
One-To-Many). The annotation map is saved in pygr.Dara first, then 
again with the schema assignment. When saving the map as schema, the 
relationship between the schema and the resources it references must 
also be made clear, and the resources must be available in pygr.Data as 
well (you must save the genome and annotations along with the 
annotation map).

@@ -235,4 +229,13 @@
     pygr.Data.ManyToManyRelation(genome,annots,bindAttrs=('annots',))

 pygr.Data.save()
-}}}
\ No newline at end of file
+}}}
+
+Accessing data is very simple:
+
+{{{
+import pygr.Data
+pygr.Data.Bio.Seq.Genome.ecoli = genome
+}}}
+
+And now the E. coli genome previously stored can be accessed and utilized!
\ No newline at end of file