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My python library of classes and functions that help me work

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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Various classes, mostly unused and out-of-date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')

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