Package: oldowan.mtconvert
oldowan.mtconvert is a small, pure Python, bioinformatic utility to (1)transform human mitochondral DNA sequence data into variant sites relative tothe revised Cambridge Reference Sequence (rCRS) and (2) transform variant sitesdata into DNA sequence. Further information on the rCRS and variant sitenomenclature for human mtDNA sequences is available at the mtconvert_ website.Installation Instructions=========================This package is pure Python and has no dependencies outside of the standardlibrary. The easist way to install is using ``easy_install`` from thesetuptools_ package.  This usually goes something like this::$ easy_install oldowan.mtconvertor 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.mtconvertYou may also use the standard python distutils setup method. Download thecurrent 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, havingdownloaded the archive and changed to the directory containing this archive inyour shell, this might go something like::$ tar xvzf oldowan.mtconvert*$ cd oldowan.mtconvert*$ python setup.py installQuick Start===========Import ``seq2sites`` and ``sites2seq`` from oldowan.mtconvert::>>> from oldowan.mtconvert import seq2sites, sites2seqConvert sequence to sites::>>> seq = """TTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACAGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCC""">>> seq2sites(seq)Sequences must be contiguous! Separate runs of sequence, such as HVR1 and HVR2without the intervening sequence interval, must be analyzed separately.There is also a cutoff on the number of ambigous sites (N) allowed in thesequence. By default, this is 10 - but this is an option that can be set::>>> seq2sites(seq, ambig_cutoff=20)Convert a list of variable sites to sequence. The default sequence region thatis returned is hypervariable region 1 (HVR1), which is positions 16024 to 16365of the rCRS (in biological one-based numbering)::>>> sites2seq('16129A 16223T')Predefined sequence regions are:- HVR1: 16024-16365- HVR2: 73-340- HVR1to2: 16024-340- coding: 577-15992- all: 1-16559So, to convert a list of HVR2 sites to sequence::>>> sites2seq('73G', region='HVR2')Sites may also be provided in a list::>>> sites2seq(['16129A', '16223T', '73G'], region='HVR1to2')The rCRS sequence will be returned given an empty string, empty list, or thestring 'rCRS'. All of the following are equivalent::>>> sites2seq('')>>> sites2seq([])>>> sites2seq('rCRS')Arbitrary positions may be selected by passing a list of sites to the``region`` option::>>> sites2seq('', region=[1,2,3])The Python range function is convenient for this, but you must remember thatthe range does not include its ending position::>>> sites2seq('', region=range(73,341))  # include 340, but not 341Release History ===============1.0.0 (March 25, 2009)initial release of module.1.0.1 (March 25, 2009)minor versioning fix1.0.2 (May 27, 2009)partial RFLP implementation1.0.3 (June 22, 2015)add fix for spurious deletions at end of query1.0.4 (June 22, 2015)improve fix for spurious deletions at end of query1.0.5 (June 22, 2015)sites outside requested region should pass silently; fix for insertions1.0.6 (August 4, 2015)fix version number install problem.. _setuptools: http://peak.telecommunity.com/DevCenter/EasyInstall