[pygr-notify] [pygr commit] r100 - wiki

codesite-noreply at google.com codesite-noreply at google.com
Wed Sep 10 00:05:12 PDT 2008 

Author: jqian.ubc
Date: Wed Sep 10 00:04:39 2008
New Revision: 100

Modified:
    wiki/PygrOnEnsembl.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/PygrOnEnsembl.wiki
==============================================================================
--- wiki/PygrOnEnsembl.wiki	(original)
+++ wiki/PygrOnEnsembl.wiki	Wed Sep 10 00:04:39 2008
@@ -65,11 +65,15 @@

  *Framework*

-*1.* the datamodel module  
[http://pygr-dev.googlegroups.com/web/datamodel.py?hl=en%253A&gsc=SDO_owsAAADv9zjLtj_JuEWS1q7AkBzo  
datamodel.py]: a BaseModel super class and its subclasses.  Each subclass  
represents a biological entity.
+*1.* the datamodel.py module
+a BaseModel super class and its subclasses.  Each subclass represents a  
biological entity.

-*2.* the adaptor module  
[http://pygr-dev.googlegroups.com/web/adaptor.py?hl=en%253A adaptor.py]: a  
driver class, a generic adaptor class (super class) and many specialized  
adaptor classes (sub classes).  Each specialized adaptor class employs pygr  
modules (mainly the sqlgraph and seqdb module) and provides access to its  
corresponding sql table in an ensembl core database.
+*2.* the adaptor.py module
+a Registry class, a generic adaptor class (super class) and many  
specialized adaptor classes (sub classes).  Each specialized adaptor class  
employs pygr modules (mainly the sqlgraph and seqdb module) and provides  
access to its corresponding sql table in an ensembl core database.

-*3.* the supporting module (seqregion.py): extensions of the pygr core  
modules.
+*3.* the featuremapping.py module
+
+*4.* the supporting module (seqregion.py): extensions of the pygr core  
modules.

  *Design Pattern*

@@ -77,73 +81,122 @@

  = Implemented Functionality =

-The current ensembl API allows the user to perform the following tasks:
+The latest ensembl API allows the user to perform the following tasks:

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

-  feature method in adaptor.py:
+Create a connection to the ensembl MySQL server:

-  - Driver: `fetch_sequence_by_region(chromosome, start, end, strand)`
+serverRegistry = get_registry(host='ensembldb.ensembl.org',  
user='anonymous')

-*2.* find all the exons, genes and transcripts in a genomic region
+Create access to an ensembl core database:

-  feature methods in adaptor.py:
+coreDBAdaptor =  
serverRegistry.get_DBAdaptor('homo_sapiens', 'core', '47_36i')

-  - ExonAdaptor: `fetch_exons_by_seqregion(chromosome, start, end, strand,  
driver)`
+Retrieve a sequence object:
+
+coreDBAdaptor.fetch_slice_by_seqregion(coordSystemName, seqregionName)

-  - GeneAdaptor: `fetch_genes_by_seqregion(chromosome, start, end, strand,  
driver)`
+-coordSystemName: 'chromosome' or 'contig'
+-seqreionName: a chromosome name, such as '1'
+	               or a contig name, such as 'AADC01095577.1.1.41877'
+-optional arguments for this method: start, end, strand

-  - TranscriptAdaptor: `fetch_transcripts_by_seqregion(chromosome, start,  
end, strand, driver)`
+Create access to any table in an ensembl core database:

-*3.* given a gene, obtain its transcripts, exons and translations
+e.g.
+transcriptAdaptor = coreDBAdaptor.get_adaptor('transcript') will return a  
transcriptAdaptor object that can be used to access any record/item in the  
transcript table.

-  feature method in datamodel.py:
+Create access to any record in an ensembl sql table:

-  - Gene: `getTranscripts()`, `getExons()`, `getTranslations()`
+e.g.
+transcript = transcriptAdaptor[1] will return a transcript item with the  
unique dbID 1

-  - Transcript: `getExons()`
+Create access to any column of an ensembl sql table record:

-  - Translation: `getExons()`
+e.g.
+transcript.seq_region_start will return the seq_region_start value of the  
give transcript

-  feature method in adaptor.py:

-  - TranscriptAdaptor: `fetch_transcripts_by_geneID(gene_id)`
+*Methods for an ensembl feature object*

-  - ExonAdaptor: `fetch_exons_by_transcriptID(transcript_id)`,  
`fetch_exons_by_translation(transcript_id, start_exon_id, end_exon_id)`
+An ensembl feature refers to an object that has the attributes of  
seq_region_id, seq_region_start, seq_region_end and seq_region_strand.

-  - TranslationAdaptor: `fetch_translations_by_transcriptID(transcript_id)`
+Retrieve the sequence of an ensembl feature:
+get_sequence()

-*4.* given an external reference label, retrieve all the associated genes
+e.g.
+gene.get_sequence() will return a sequence object of the given gene.

-  feature method in adaptor.py:
+optional argument for this method: the lengh of the flanking region on  
both sides of the feature sequence:

-  - GeneAdaptor: `fetch_genes_by_externalRef(external_ref_label)`
+e.g.
+gene.get_sequence(500) will return the sequence of the gene plus 500bp  
flanking regions on both sides of the gene.

+Find all the feature objects in a particular slice:

-*5.* obtain the DNA sequence of a particular sliceable object (such as a  
gene, a transcript or an exon)
+fetch_all_by_slice(slice)

-  feature method in datamodel.py:
+e.g.
+transcriptAdaptor.fetch_all_by_slice(slice) will retrieve all the  
transcripts in the give slice.

-  - Sliceable: `getSequence(table_name)`
-             	
-*6.* obtain a column-value attribute associated with a table-record object
+Retrieve the stable_id, created_date, modified_date or the version for a  
gene/transcript/translation/exon

-= Updates =
+e.g.
+gene.get_stable_id() will return the ensembl stable_id for the given gene

-*1.* mini-release upgraded to v0.03
+Obtain a gene object:

-ensemblv0.03.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])
+transcript.get_gene()
+geneAdaptor.fetch_by_stable_id(geneStableID)

-Alternatively, the current ensembl API code, together with pygr, can be  
retrieved from the public git repository.  To check out a copy, run the  
following instruction on the command line:
+Obtain transcript objects:

-`git clone git://iorich.caltech.edu/git/public/pygr-jenny <dirname of your  
choice>`
+gene.get_transcripts()
+exon.get_all_transcripts()
+translation.get_transcript()
+transcriptAdaptor.fetch_by_stable_id(transcriptStableID)
+
+Obtain exon objects:
+
+transcript.get_all_exons()
+exonAdaptor.fetch_by_stable_id(exonStableID)
+
+Obtain a translation object:
+
+transcript.get_translation()
+translationAdaptor.fetch_by_stable_id(translationStableID)
+
+Obtain a spliced sequence object:
+
+transcript.get_spliced_seq()
+
+Obtain a five-prime untranslated region:
+
+transcript.get_five_utr()

-(More information on Git can be found at  
[http://code.google.com/p/pygr/wiki/UsingGit UsingGit])
+Obtain a three-prime untranslated region:

-*2.* the test output files
+transcript.get_three_utr()

-They provide a preliminary test outcome for the functions implemented.
+Obtain a prediction_transcript object:

-[http://pygr-dev.googlegroups.com/web/testdatamodel.out?hl=en%253A:  
testdatamodel.out] from running the sample code in datamodel.py, which  
gives a test result for the functions implemented in each specialized  
Datamodel class.
+predictionExon.get_prediction_transcript()
+
+Obtain prediction_exon objects:
+
+predictionTranscript.get_all_prediction_exons()
+
+
+Additional sample code can be found under major methods in both the  
adaptor.py module and the datamodel.py module, in the form of doctests.
+
+= Updates =
+
+*1.* The latest Ensembl API tarball Qing_Qian.tar.gz can be downloaded  
from  
[http://code.google.com/p/google-summer-of-code-2008-psf/downloads/list#].
+For the prerequisites and installation details, please refer to the README  
file.
+
+Alternatively, the current ensembl API code, together with pygr, can be  
retrieved from the public git repository.  To check out a copy, run the  
following instruction on the command line:
+
+`git clone git://iorich.caltech.edu/git/public/pygr-jenny <dirname of your  
choice>`

-[http://pygr-dev.googlegroups.com/web/testadaptor.out?hl=en%253A:  
testadaptor.out] from running the sample code in adaptor.py, which gives a  
test result for the functions implemented in the Driver class and in each  
specialized Adaptor class.
\ No newline at end of file
+(More information on Git can be found at  
[http://code.google.com/p/pygr/wiki/UsingGit UsingGit])
\ No newline at end of file

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