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My python library of classes and functions that help me work

Project Description

`|Build Status| <https://travis-ci.org/childsish/lhc-python>`_

lhc-python
==========

This is my personal library of python classes and functions, many of
them have bioinformatics applications. The library changes constantly
and at a whim. If you want to use it, approach with caution. Over time
however, parts appear to be settling on a stable configuration.

lhc.binf
--------

**lhc.binf.alignment**

A pure Python implementation of the Smith-Waterman local alignment
algorithm.

**lhc.binf.digen**

A C++ and pure Python implementation of sequence generation algorithm.
The generated sequence will have a specified dinucleotide frequency.

**lhc.binf.genomic\_coordinate**

An implementation of intervals and points for genomic coordinates.
Useful for representing gene models.

**lhc.binf.genetic\_code**

A class to read genetic codes and translate DNA sequences into protein
sequences

**lhc.binf.iupac**

A class to convert protein names between the one and three letter codes
and the full name.

**lhc.binf.kmer**

A class that calculates k-mers for a given sequence. The class behaves
likea dict, but calculates new k-mers on the fly.

**lhc.binf.skew**

A class that calculates skews for a given sequence. The class behaves
like a dict, but calculates new skews on the fly.

lhc.collections
---------------

Several collections mostly for holding intervals. If only intervals need
to be held, use the IntervalTree, otherwise the MultiDimensionMap may be
more appropriate.

lhc.filetools
-------------

Classes for working with files

lhc.graph
---------

A pure Python implementation of graphs

lhc.indices
-----------

Intended to be my own code for indexing files but is still very unstable
an immature

lhc.interval
------------

A class for intervals and interval operations

lhc.io
------

Classes for parsing and working with several file formats

lhc.itertools
-------------

Classes for working with iterators

lhc.tools
---------

Various classes, mostly unused and out-of-date

lhc.random
----------

**lhc.random.reservoir**

An implementation of the reservoir sampling algorithm. Can also be run
from the command line to sample lines from files. To sample 50 lines
from a file called input\_file.txt, run:

::

python -m lhc.random.reservoir input_file.txt 50

lhc.stats
---------

Really old code. Probably the NIPALS and PCA algorithms are of most use.

lhc.test
--------

Unit tests! These should be mostly up-to-date now.

lhc.tools
---------

**lhc.tools.sorter**

A sorter for very large iterators. The iterator will be split into
chunks which are then sorted individually and then merged into a single
file.

**lhc.tools.tokeniser**

A basic tokeniser. Users define which characters belong to which classes
and the tokeniser will split strings into substrings where all
characters have the same type.

::

>>> tokeniser = Tokeniser({'word': 'abcdefghijklmnopqrstuvwxyz',
'number': '0123456789',
'space': ' \t'})
>>> tokens = tokeniser.tokenise('there were 1000 bottles on the wall')
>>> tokeniser.next()
Token(type='word', value='there')
>>> tokeniser.next()
Token(type='space', value=' ')
>>> tokeniser.next()
Token(type='word', value='were')
>>> tokeniser.next()
Token(type='space', value=' ')
>>> tokeniser.next()
Token(type='number', value='1000')

.. |Build
Status| image:: https://travis-ci.org/childsish/lhc-python.svg?branch=master

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