[pygr-notify] [pygr commit] r40 - wiki

[codesite-noreply at google.com]

Author: ramccreary
Date: Mon Jun 16 21:02:37 2008
New Revision: 40

Modified:
   wiki/pygrDataIntroduction.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/pygrDataIntroduction.wiki
==============================================================================
--- wiki/pygrDataIntroduction.wiki	(original)
+++ wiki/pygrDataIntroduction.wiki	Mon Jun 16 21:02:37 2008
@@ -9,24 +9,32 @@

  	The module seqdb is first imported because pygr.Data needs the data 
to be stored in a container, and, since an E. coli genome sequence is 
used in this example,  the sequence is stored in a BLAST database using 
seqdb. BLAST (Basic Local Alignment Search Tool) databases are designed 
for storing sequence alignments.

+{{{
 from pygr import seqdb
-
+}}}

  	pygr.Data is then imported to allow access to the data namespace. 
This is an essential step, as pygr.Data must be previously imported in 
order to store or access data from or in it. PYGRPDATAPATH must be set 
to the directory in which it is located.

+{{{
 import pygr.Data

+}}}
  	In the following step, the data is stored in a container. There are 
many options for this , including a MySQL table or a BLAST database as 
seen here.

+{{{
 ecoli = seqdb.BlastDB('/home/mccreary/Projects/pygr/data/CP000802.fna')
-
+}}}

  	The next line is extremely important, as the data MUST have a __doc__ 
string which describes the kind of data it is, so that when a user 
looks at a directory listing of pygr.Data, he/she can quickly ascertain 
what data is stored. A __doc__string (documentation string) allows 
users to easily associate documentation with functions, classes, and 
modules, which is especially convenient for pygr.Data, since many 
databases could potentially be stored in it, and documentation ensures 
clarity and unambiguity.

+{{{
 ecoli.__doc__ = 'ecoli genome sequence'
+}}}

  	Finally, the data is stored in pygr.Data using the save() function. 
In all pygr.Data sessions, it is essential to call the pygr.Data.save() 
function to ensure all new data that has been added that session is 
committed. Furthermore, it is imperative to observe the naming 
conventions for saving data to pygr.Data, since not only does it assign 
a unique and consistent name to the data, ensuring its easy import, but 
also since multiple users could be using one pygr.Data database and the 
data should be clearly organized.

+{{{
 pygr.Data.Bio.Seq.Genome.ECOLI.ecoli = ecoli

-pygr.Data.save()
\ No newline at end of file
+pygr.Data.save()
+}}}
\ No newline at end of file