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https://github.com/greenelab/django-genes

A Django package to represent genes
https://github.com/greenelab/django-genes

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A Django package to represent genes

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README 

        

Genes

*****



Genes is a Django app to represent genes.



Download and Install

====================



This package is registered as ``django-genes`` in PyPI and is pip

installable:



::



   pip install django-genes



If any of the following dependency packages are not found on your

system, ``pip`` will install them too:



* ``django 1.8 or later`` (Django web framework)



* ``django-organisms`` (``Organisms`` model, which is required by

  ``Genes`` model)



* ``django-haystack`` (see ``Search Indexes and Data Template``

  section.)



* ``django-fixtureless`` (for unittest, see ``tests.py``)



Quick Start

===========



1. Add **'genes'** and **'organisms'** to your ``INSTALLED_APPS``

setting like this:



::



   INSTALLED_APPS = (

       ...

       'organisms',

       'genes',

   )



2. Run ``python manage.py migrate`` command to create ``genes`` and

``organisms`` models.



3. **(Optional)** The following step is only needed if you have

django-tastypie installed to create a REST API for your project and

would like to have API endpoints for ``django-organisms`` and

``django-genes``.



Add the following to your project's ``urls.py`` file:



::



   # There are probably already other imports here, such as:

   # from django.conf.urls import url, patterns, include



   # If you have not already done so, import the tastypie API:

   from tastypie.api import Api



   # Import the API Resources for Organisms and Genes:

   from organisms.api import OrganismResource

   from genes.api import GeneResource



   # If you have not already done so, initialize your API and

   # add the Organism and Gene Resources to it. You can also register

   # the CrossRefResource and CrossRefDBResource if you want to have

   # API endpoints for them as well.

   v0_api = Api()

   v0_api.register(OrganismResource())

   v0_api.register(GeneResource())

   v0_api.register(CrossRefResource())

   v0_api.register(CrossRefDBResource())



   # In the urlpatterns, include the urls for this api:

   urlpatterns = patterns('',

       ...

       (r'^api/', include(v0_api.urls))

   )



Search Indexes and Data Template

================================



The module ``search_indexes.py`` can be used by **django haystack**

(https://github.com/django-haystack/django-haystack) to search genes.

It includes the Gene fields that should be included in the search

index, and how they should be weighted. The ``text`` field refers to a

document that is built for the search engine to index. The location of

data template for this document is:

``genes/templates/search/indexes/gene_text.txt``.



For more information, see:

http://django-haystack.readthedocs.org/en/latest/tutorial.html#handling-data



Usage of Management Commands

============================



This app includes five management commands in ``management/commands/``

sub-directory:



1. genes_add_xrdb

-----------------



..



   This command adds cross-reference databases for genes. It **must**

   be called for every new cross-reference database to populate the

   gene and cross-reference objects in the database. It requires 2

   arguments:



   * name: the name of the database



   * URL: the URL for that database, with the string '_REPL_' added at

     the end of the URL



   For example, this command adds Ensembl as a cross-reference

   database:



   ::



      python manage.py genes_add_xrdb --name=Ensembl --URL=http://www.ensembl.org/Gene/Summary?g=_REPL_



   And this command adds MIM as a cross-reference database:



   ::



      python manage.py genes_add_xrdb --name=MIM --URL=http://www.ncbi.nlm.nih.gov/omim/_REPL_



2. genes_load_geneinfo

----------------------



..



   This command parses gene info file(s) and saves the corresponding

   gene objects into the database. It takes 2 required arguments and 5

   optional arguments:



   * (Required) geneinfo_file: location of gene info file;



   * (Required) taxonomy_id: taxonomy ID for organism for which genes

     are being populated;



   * (Optional) gi_tax_id: alternative taxonomy ID for some organisms

     (such as S. cerevisiae);



   * (Optional) symbol_col: symbol column in gene info file. Default

     is 2;



   * (Optional) systematic_col: systematic column in gene info file.

     Default is 3;



   * (Optional) alias_col: the column containing gene aliases. If a

     hyphen '-' or blank space ' ' is passed, symbol_col will be used.

     Default is 4.



   * (Optional) put_systematic_in_xrdb: name of cross-reference

     Database for which you want to use organism systematic IDs as

     CrossReference IDs. This is useful for Pseudomonas, for example,

     as systematic IDs are saved into PseudoCAP cross-reference

     database.



   The following example shows how to download a gzipped human gene

   info file from NIH FTP server, and populate the database based on

   this file.



   ::



      # Create a temporary data directory:

      mkdir data



      # Download a gzipped human gene info file into data directory:

      wget -P data/ -N ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz



      # Unzip downloaded file:

      gunzip -c data/Homo_sapiens.gene_info.gz > data/Homo_sapiens.gene_info



      # Call genes_load_geneinfo to populate the database:

      python manage.py genes_load_geneinfo --geneinfo_file=data/Homo_sapiens.gene_info --taxonomy_id=9606 --systematic_col=3 --symbol_col=2



3. genes_load_uniprot.py

------------------------



..



   This command can be used to populate database with UniProtKB

   identifiers. It takes one argument:



   * uniprot_file: location of a file mapping UniProtKB IDs to Entrez

     and Ensembl IDs



   **Important:** Before calling this command, please make sure that

   both Ensembl and Entrez identifiers have been loaded into the

   database.



   After downloading the gzipped file, use ``zgrep`` command to get

   the lines we need (the original file is quite large), then run this

   command:



   ::



      wget -P data/ -N ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping.dat.gz

      zgrep -e "GeneID" -e "Ensembl" data/idmapping.dat.gz > data/uniprot_entrez_ensembl.txt

      python manage.py genes_load_uniprot --uniprot_file=data/uniprot_entrez_ensembl.txt



4. genes_load_wb.py

-------------------



..



   This command can be used to populate database with WormBase

   identifiers. It takes 3 arguments:



   * (Required) wb_url: URL of wormbase xrefs file;



   * (Optional) db_name: the name of the cross-reference database,

     default is 'WormBase'.



   As is expected, the WormBase cross-reference database should be

   populated using the ``genes_add_xrdb`` command (see command #1)

   before this command to populate the WormBase identifiers. Here is

   an example:



   ::



      # Find latest version of WormBase here:

      # http://www.wormbase.org/about/release_schedule#102--10-1

      python manage.py genes_load_wb --wb_url=ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS243.xrefs.txt.gz



5. genes_load_gene_history.py

-----------------------------



..



   This management command will read an input gene history file and

   find all genes whose tax_id match input taxonomy ID. If the gene

   already exists in the database, the Gene record in database will be

   set as obsolete; if not, a new obsolete Gene record will be created

   in the database.



   The command accepts 2 required arguments and 3 optional arguments:



   * (Required) gene_history_file: Input gene history file. A gzipped

     example file can be found at:

     ftp://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz



   * (Required) tax_id: Taxonomy ID assigned by NCBI to a certain

     organism. Genes of the other organisms in input file will be

     skipped.



   * (Optional) tax_id_col: column number of tax_id in input file.

     Default is 1.



   * (Optional) discontinued_id_col: column number of discontinued

     GeneID in input file. Default is 3.



   * (Optional) discontinued_symbol_col: column number of gene's

     discontinued symbol in input file. Default is 4.



   Note that column numbers in the last three arguments all start from

   1, **not** 0.



   For example, to add obsolete genes whose tax_id is 208964 in the

   file "gene_history", we will use the command like this:



   ::



      # Download file into your data directory:

      cd /data_dir; wget ftp://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz



      # Unzip the downloaded file into "gene_history"

      gunzip gene_history.gz



      # Run management command:

      python manage.py genes_load_gene_history /data_dir/gene_history 208964 --tax_id_col=1 --discontinued_id_col=3 --discontinued_symbol_col=4



   (Here ``--tax_id_col=1 --discontinued_id_col=3

   --discontinued_symbol_col=4`` are optional because they are using

   default values.)