Search with FM-Index

This example loads a file.fasta file and creates an index file.fmindex. If the index already exists it is loaded from disk. The programs continues to search for "AA". The results depend on the contents of file.fasta

import iv2py as iv
import os

# load index or create an index
if os.path.exists("file.fmindex"):
    # load fm index from disk
    index = iv.fmindex(path="file.fmindex")
else:
    # load fasta file - normalize sequences (e.g.: make everything capital letters, check for invalid characters)
    reference = [iv.normalize(rec.seq) for rec in iv.fasta.reader("file.fasta")]

    # build fmindex
    index = iv.fmindex(reference=reference, samplingRate=16)

    index.save("file.fmindex")

# search through fmindex
res = index.search("CG")
print(res)

# search through fmindex with errors
res2 = index.search("CG", k=1)

file.fasta:

>name1
AACCGGTT
>name2
acgtacgt

output:

[(0, 3), (1, 5), (1, 1)]