FM-Index

An FM-Index is a data structure that supports fast searches for exact searches.

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Functions and classes

• iv2py.fmindex
• iv2py.fmindex.load
• iv2py.fmindex.search
• iv2py.fmindex.save

Example usages

Construct & SearchConstruct & SaveLoad & Search

Constructs an fmindex and searches for all occurences of "CG".

import iv2py as iv

reference = ["AACCGGTT", "ACGT"]
index = iv.fmindex(reference=reference, samplingRate=16)

result = index.search("CG")
print(result)

"""search with errors"""
result2 = index.search("CG", k=1);

Output:

[(0, 3), (1, 1)]

Constructs an fmindex an saves it to disk.

import iv2py as iv

reference = ["AACCGGTT", "ACGT"]
index = iv.fmindex(reference=reference, samplingRate=16)
index.save("myindex.idx")

Loads an fmindex and searches for all occurences of "CG".

import iv2py as iv

index = iv.fmindex(path="myindex.idx")

result = index.search("CG")
print(result)

"""search with errors"""
result2 = index.search("CG", k=1);

Output:

[(0, 3), (1, 1)]