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: dev@intermine.org

== License

All code in this project is dual licensed under the LGPL version 3 license and the BSD 2-clause license