============
 Metascript
============

by Michael Hoffman <hoffman+python-software@ebi.ac.uk>

Prerequisites
=============
Bits of this package are written for use with Jython or CPython:

CPython
-------
* CPython 2.5.1 <http://www.python.org/>
* Enstag 0.1.1 <http://www.ebi.ac.uk/~hoffman/software/enstag/>
* Biopython

Jython
------
* Jython 2.1 <http://www.jython.org/>
* Ensj 39.2 <http://cvs.sanger.ac.uk/cgi-bin/cvsweb.cgi/ensj-web/build/ensj-39.2.jar?rev=1.1&view=auto>
* Ensj/Jython 39.2 <http://cvs.sanger.ac.uk/cgi-bin/cvsweb.cgi/ensj-web/build/ensj-39.2-src_jython.zip?rev=1.1&view=auto>
* Enstag 0.1.1 (must be installed for Jython as well)

Other
-----
* Wise2 from CVS (cvs -d :pserver:cvsuser@cvsro.sanger.ac.uk:/cvsroot/CVSmaster co wise2)

Installation
============
Jython 2.1 does not come with the sophisticated package installation
system that newer versions of CPython have. I have put together an
ad-hoc script, javasetup.py that will attempt to install things in
sys.path[2]. If you want the Jython package installed elsewhere,
please edit INSTALL_DIR in javasetup.py.

jython javasetup.py build
jython javasetup.py install
python setup.py build
python setup.py install

Running Metascript
==================

get_metascripts
---------------
usage: get_metascripts [OPTION...] FILE

FILE is a text file, with each line being a tab-delimited list of
homologous Enstags. It is necessary to use Enstags instead of vanilla
Ensembl accession IDs because they fully encode information about
species to be used.

Use get_metascripts --help to get a full list of options.

Note
====
Ensj is no longer officially supported by Ensembl. At some point it
may stop working, and so will the Jython portions of Metascript.

Citation
========
Michael M. Hoffman and Ewan Birney. 2007. "Estimating the Neutral Rate
of Nucleotide Substitution Using Introns." Molecular Biology and
Evolution 24(2):522-531.

<http://mbe.oxfordjournals.org/cgi/content/abstract/24/2/522>
