README

Command line scripts for the oldowan.mitomotifs package.

oldowan.mitomotifs-cmdline provides the ``seq2sites`` and ``sites2seq`` command
line scripts to covert human mitochondrial DNA sequences to lists of variant
sites relative to the revised Cambridge Reference Seqeunce and vice versa.
Further information on the rCRS and variant site nomenclature for human mtDNA
sequences is available at the MitoMotifs_ website. 

This package is only the command line extension of the core oldwan.mitomotifs
module. If you want just the Python libraries and not the command line tools,
you should go directly to that package.

Installation Instructions
=========================

This package is pure Python and has only pure Python dependencies
(oldowan.mitomotifs and oldowan.fasta) outside of the standard library. All of
these dependencies will be automatically installed if you use the setuptools_
``easy_install`` tool.  This usually goes something like this::

	$ easy_install oldowan.mitomotifs-cmdline

or on a unix-like system, assuming you are installing to the main Python
``site-packages`` directory as a non-privileged user, this::

	$ sudo easy_install oldowan.mitomotifs-cmdline

You may also use the standard python distutils setup method. You will have to
download ind install oldowan.fasta and oldowan.mitomotifs first. Then, download
the current source archive from the file list towards the bottom of this page,
unarchive it, and install. On Mac OS X and many other unix-like systems, having
downloaded the archive and changed to the directory containing this archive in
your shell, this might go something like::

	$ tar xvzf oldowan.mitomotifs-cmdline*
	$ cd oldowan.mitomotifs-cmdline*
	$ python setup.py install

Quick Start
===========

Convert sequences to sites::

  $ seq2sites sequences.fasta

Convert sequences to sites, saving the output to a file::

  $ seq2sites sequences.fasta > sites.txt

Sequences must be contiguous! Separate runs of sequence, such as HVR1 and HVR2
without the intervening sequence interval, must be analyzed separately.

There is also a cutoff on the number of ambigous sites (N) allowed in the
sequence. By default, this is 10 - but this is an option that can be set::

  $ seq2sites --ambig-cutoff=20 sequences.fasta

Convert a list of variable sites to sequence. The input file should be a
comma-seprated-values list with one entry per line, with name, N, and sites.
Sites should be separated by whitespace::

  $ cat hvr1_sites.txt
  Seq1,1,16129A
  Seq2,1,16129A 16223T
  Seq3,2,16223T
  $ sites2seq hvr1_sites.txt

The default range of sequence returned is HVR1, defined as positions 16023 to
16365 on the rCRS. All predefined ranges are:

- HVR1: 16024-16365
- HVR2: 73-340
- HVR1to2: 16024-340
- coding: 577-15992
- all: 1-16559

So, to convert a list of HVR2 sites to sequence::

  $ sites2seq --region=hvr2 hvr2_sites.txt

An arbitrary range may be selected. If the stop value is smaller than the
start, it is assumed that the range runs through the origin::

  $ sites2seq --begin=16024 --end=340 dloop_sites.txt

The rCRS sequence will can be selected with 'rCRS' as the sites value::

  $ cat sites.txt
  Seq1,1,rCRS
  Seq2,1,16129A 16223T

Release History ===============

1.0.0 (August 16, 2008)
    initial release of module.


.. _MitoMotifs: http://mitomotifs.raaum.org
.. _setuptools: http://peak.telecommunity.com/DevCenter/EasyInstall