[pygr-notify] [pygr commit] r58 - wiki

[codesite-noreply at google.com]

Author: jqian.ubc
Date: Tue Jun 24 11:51:34 2008
New Revision: 58

Modified:
   wiki/PygrOnEnsembl.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/PygrOnEnsembl.wiki
==============================================================================
--- wiki/PygrOnEnsembl.wiki	(original)
+++ wiki/PygrOnEnsembl.wiki	Tue Jun 24 11:51:34 2008
@@ -62,34 +62,40 @@

  *1.* obtain the DNA sequence of a particular genomic region (defined 
by chromosome, start, end and strand)

-     feature method in adaptor.py:
-     - Driver: fetch_sequence_by_region(chromosome, start, end, strand)
+  feature method in adaptor.py:
+
+  - Driver: fetch_sequence_by_region(chromosome, start, end, strand)

 *2.* find all the exons, genes and transcripts in a genomic region

-     feature methods in adaptor.py:
-     - ExonAdaptor: fetch_exons_by_seqregion(chromosome, start, end, 
strand, driver)
+  feature methods in adaptor.py:
+
+  - ExonAdaptor: fetch_exons_by_seqregion(chromosome, start, end, 
strand, driver)
+
+  - GeneAdaptor: fetch_genes_by_seqregion(chromosome, start, end, 
strand, driver)

-         - GeneAdaptor: fetch_genes_by_seqregion(chromosome, start, 
end, strand, driver)
+  - TranscriptAdaptor: fetch_transcripts_by_seqregion(chromosome, 
start, end, strand, driver)

-         - TranscriptAdaptor: 
fetch_transcripts_by_seqregion(chromosome, start, end,
-           strand, driver)
+  feature method in datamodel.py:

-     feature method in datamodel.py:
-     - Sliceable: getExons()
+  - Sliceable: getExons()

  *3.* obtain the DNA sequence of a particular sliceable object (such as 
a gene, a transcript or an exon)

-     feature method in datamodel.py:
-         - Sliceable: getSequence(table_name)
+  feature method in datamodel.py:
+
+  - Sliceable: getSequence(table_name)
              	
 *4.* obtain a column-value attribute associated with a table-record object

 = Updates =

-*1.* mini-release upgraded v0.02 *ensemblv0.02.tar.gz* at 
[http://groups.google.com/group/pygr-dev/files?hl=en: pygr-dev files] 
(running environment: the latest pygr.  For detailed information on how 
to get a copy of it, please go to 
[http://code.google.com/p/pygr/wiki/ViewSource ViewSouce])
+*1.* mini-release upgraded to v0.02
+
+ensemblv0.02.tar.gz at 
[http://groups.google.com/group/pygr-dev/files?hl=en: pygr-dev files] 
(running environment: the latest pygr.  For detailed information on how 
to get a copy of it, please go to 
[http://code.google.com/p/pygr/wiki/ViewSource ViewSouce])

 *2.* the test output files
+
 They provide a preliminary test outcome for the functions implemented.

  [http://pygr-dev.googlegroups.com/web/testdatamodel.out?hl=en: 
testdatamodel.out] from running the sample code in datamodel.py, which 
gives a test result for the functions implemented in each specialized 
Datamodel class.