[pygr-notify] [pygr commit] r67 - wiki

[codesite-noreply at google.com]

Author: ramccreary
Date: Tue Jul  8 09:41:10 2008
New Revision: 67

Modified:
   wiki/DataStorageUsingpygr.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/DataStorageUsingpygr.wiki
==============================================================================
--- wiki/DataStorageUsingpygr.wiki	(original)
+++ wiki/DataStorageUsingpygr.wiki	Tue Jul  8 09:41:10 2008
@@ -11,7 +11,7 @@

  The OptionParser class, taken from the optparse module, processes 
command line arguments. The filenames ( a .fna file and .gff file, in 
this case) are supplied by attributing them to an option name in the 
command line. If the attribute for either option is 'None', indicating 
there was no filename supplied, the help text for optparse will be 
printed, as well as the available option names. The option for each 
file was added, then given a name that would represent it during parsing.

-In this step, the genome is loaded into the annotation database. The 
BlastDB module establishes a BLAST database for the genome.
+In this step, the genome is loaded into a BLAST database. The BlastDB 
module establishes a BLAST database for the genome.

 {{{
 #! /usr/bin/env python
@@ -174,10 +174,11 @@

  Finally, the MySQL database for the annotation is built, and saved as 
the supplied database name. conn.commit() closes the database and the 
transaction and makes the changes permanent.

+Here, slicedb uses the annotation objects from the SQLTable, which 
correspond to the gene sequences in the BLAST database previously 
constructed that contains the genome. AnnotationDB uses the annotations 
as keys within a dictionary, and the values are the annotation objects, 
which are similar to sequence intervals in that they represent segments 
of the genome, but have annotation data associated with them. The two 
containers supplied for AnnotationDB are the slicedb, which contains 
the SQL table that holds the list of annotation objects, and sequence 
database for the E. coli sequence that holds the sequence intervals.

-Here, slicedb uses the annotation objects from the SQLTable, which 
correspond to the gene sequences in the BLAST database previously 
constructed that contains the genome. AnnotationDB uses the sequence 
intervals are keys within a dictionary, and the values are the 
annotation objects, which are similar to sequence intervals in that 
they represent segments of the genome, but have annotation data 
associated with them. The two containers supplied for AnnotationDB are 
the slicedb, which contains the SQL table that holds the list of 
annotation objects, and sequence database for the E. coli sequence.
+It should be noted that the sequence intervals and the annotation 
objects are NOT stored in the same database. The annotations and their 
corresponding IDs are stored within the annotation database, while the 
related sequence intervals are stored within the sequence database, 
also with their own IDs. However, the annotation objects have a 
sequence attribute that enables the annotation's matching sequence 
interval to be given as well.

-Then, a dictionary is created to hold the annotation database and the 
genome database together. PrefixUnionDict provides a cohesive interface 
to access the data in the two databases.
+Then, a dictionary is created to hold the annotations and the 
sequences they correspond to together. PrefixUnionDict provides a 
cohesive interface to access the data in the two databases.


  Finally, an annotation map is created, with the annotations added. The 
nested list format for data structure shortens the time needed to scan 
the intervals by storing overlapping intervals in a more efficient and 
hierarchal format. The annotations are then mapped to the segment of 
the genome to which they correspond.