[pygr-notify] [pygr commit] r64 - wiki

[codesite-noreply at google.com]

Author: jqian.ubc
Date: Wed Jul  2 13:49:31 2008
New Revision: 64

Modified:
   wiki/PygrOnEnsembl.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/PygrOnEnsembl.wiki
==============================================================================
--- wiki/PygrOnEnsembl.wiki	(original)
+++ wiki/PygrOnEnsembl.wiki	Wed Jul  2 13:49:31 2008
@@ -83,29 +83,46 @@

   feature method in adaptor.py:

-  - Driver: fetch_sequence_by_region(chromosome, start, end, strand)
+  - 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)
+  - 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)`
+
+*3.* given a gene, obtain its transcripts, exons and translations

   feature method in datamodel.py:

-  - Sliceable: getExons()
+  - Gene: `getTranscripts()`, `getExons()`, `getTranslations()`
+
+  feature method in adaptor.py:
+
+  - TranscriptAdaptor: `fetch_transcripts_by_geneID(gene_id)`
+
+  - ExonAdaptor: `fetch_exons_by_transcriptID(transcript_id)`, 
`fetch_exons_by_translation(transcript_id, start_exon_id, end_exon_id)`
+
+  - TranslationAdaptor: `fetch_translations_by_transcriptID(transcript_id)`
+
+*4.* given an external reference label, retrieve all the associated genes
+
+  feature method in adaptor.py:
+
+  - GeneAdaptor: `fetch_genes_by_externalRef(external_ref_label)`
+

-*3.* obtain the DNA sequence of a particular sliceable object (such as 
a gene, a transcript or an exon)
+*5.* 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)
+  - Sliceable: `getSequence(table_name)`
              	
-*4.* obtain a column-value attribute associated with a table-record object
+*6.* obtain a column-value attribute associated with a table-record object

 = Updates =