Leverages the Burrows-Wheeler compression of BZip to estimate the complexity/information density of a sequence
Project description
bzComplexityAnalyzer
Getting Started
import bzComplexityAnalyzer
Preparing an analyzer object
analyzer = bzComplexityAnalyzer.Analyzer(alphabet="dna", ignoreCase=True, iterations=1000)
- alphabet: string or list of characters Specifies the alphabet to be compared against. Default: DNA
- ignoreCase: boolean If true, casing of letters will be homogenized before analysis to neutralize their effects on complexity
- iterations int Number of random sequences to use for finding the distribution of compressed product lengths
Estimating the complexity of a sequence
analyzer.getCompressionZScore("GAATTCGAATTCGAATTC") # Returns a Z-score
analyzer.getCompressionPercentile("GAATTCGAATTCGAATTC") # Returns a percentile
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