[pygr-notify] [pygr commit] r70 - wiki

[codesite-noreply at google.com]

Author: ramccreary
Date: Tue Jul  8 14:25:42 2008
New Revision: 70

Modified:
   wiki/GenomeCalculationsUsingpygr.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/GenomeCalculationsUsingpygr.wiki
==============================================================================
--- wiki/GenomeCalculationsUsingpygr.wiki	(original)
+++ wiki/GenomeCalculationsUsingpygr.wiki	Tue Jul  8 14:25:42 2008
@@ -17,7 +17,7 @@
 import re
 }}}

-Once everything is imported, the focus turns to interpreting the .gff 
file used in this example. One of the initial problems I had was 
defining the id. AnnotationDB needs at least an ID, as well as the 
start and stop values. However, the sequence ID is the same for each 
annotation, and something was needed to serve as a unique reference for 
each annotation that mapped to a different sequence. I noticed that the 
locus_tag=EcHS_A(number) was unique for each Genbank Gene, Regular 
Expression was used to search through the annotations, and store each 
annotation and its corresponding data if the locus tag was unique.
+Once everything is imported, the focus turns to interpreting the .gff 
file used in this example. One of the initial problems I had was 
defining the id. AnnotationDB needs at least an ID, as well as the 
start and stop values. However, the annotation ID is the same for each 
annotation, and something was needed to serve as a unique reference for 
each annotation that mapped to a different sequence. I noticed that the 
locus_tag=EcHS_A(number) was unique for each Genbank Gene, Regular 
Expression was used to search through the annotations, and store each 
annotation and its corresponding data if the locus tag was unique.

  The class EcoliGene was defined to clarify each row and the 
information contained within. The orientation was specified by 
assigning a negative value to the start and stop values. If the start 
and stop values were 349 and 915 but the value of 'strand' was -1, the 
values assigned for start and stop would be-349 and -915.