https://github.com/alexkalderimis/intermine-ws-bio-python

Bio Extensions for the Python WS client
https://github.com/alexkalderimis/intermine-ws-bio-python

Last synced: 11 days ago
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Bio Extensions for the Python WS client

• Host: GitHub
• URL: https://github.com/alexkalderimis/intermine-ws-bio-python
• Owner: alexkalderimis
• License: lgpl-3.0
• Created: 2011-10-17T00:45:26.000Z (over 13 years ago)
• Default Branch: master
• Last Pushed: 2011-10-17T00:45:50.000Z (over 13 years ago)
• Last Synced: 2024-04-09T22:22:37.209Z (10 months ago)
• Language: Python
• Homepage: www.intermine.org
• Size: 102 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README
  • Changelog: Changes
  • License: COPYING.txt

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README

        
= Biological Extensions to the InterMine Webservice Client Library 

This library is a set of extensions to the InterMine Webservices client, 

providing access for data in biological formats. It provides 

a wrapper class interminebio.SequenceQuery that can be used to gain access

to biologically specific data.

== Example

Get all sequences for proteins on "h", "r", "eve", "bib" and "zen":

    from intermine.webservice import Service

    from interminebio import SequenceQuery

    s = Service("www.flymine.org/query")

    q = SequenceQuery(s, "Gene")

    syms = ["h", "r", "eve", "bib", "zen"] 

    print q.select_sequence("proteins").where(s.model.Gene.symbol == syms).fasta()

Process the locations of these genes one at a time:

    for line in q.select_sequence("Gene").where(s.model.Gene.symbol == syms).bed():

        process(line)

== Who is this for?

InterMine data warehouses are typically constructed to hold

Biological data, and as this library facilitates programmatic

access to these data, this install is primarily aimed at 

bioinformaticians. In particular, users of the following services

may find it especially useful:

 * FlyMine (http://www.flymine.org/query)

 * YeastMine (http://yeastmine.yeastgenome.org/yeastmine)

 * RatMine (http://ratmine.mcw.edu/ratmine)

 * modMine (http://intermine.modencode.org/release-23)

 * metabolicMine (http://www.metabolicmine.org/beta)

These extensions are aimed at bioinformaticians looking to integrate

these sources of data into other workflows.

For details on constructing queries, see the intermine documentation.

== Support

Support is available on our development mailing list: [email protected]

== License

This code is Open Source under the LGPL. Source code for all InterMine code

can be checked out from svn://subversion.flymine.org/flymine