Functions give different results

[AnnaNenarokova]

Hi! I was looking for a suitable tool for Python for a long time, and was very pleased to find your package. Thank you for it. I have a question about results of functions. I tried this:

seq = 'NAGGTTGGTGGGTTGTTTTTATGGGATAAAATGCTTTAAGAACAAATGTATACTTTTAGAGAGTTCCCCGCGCCAGCGGGGATAAACCGTTGTCTTTCGCTGCTGAGGGTGACGATCCCGCGAGTTCCCTGCGCCAGGGGGGATAAACCGCTTTCGCAGACGCGCGGCGATACGCTCACGCAGAGTTGCCCGCGCCAGCGGGGATCAACCGCAGCCGAAGGCAAAGGTGATGACGAGATTGGAAGAGCGG'
subseq = 'GAGTTCCCCGCGCCAGCGGGGATAAACCGC'
for max_distance in range(5):
    print (find_near_matches(subseq, seq, max_distance))

It returns:

[]
[Match(start=60, end=90, dist=1)]
[Match(start=60, end=90, dist=1), Match(start=121, end=151, dist=2), Match(start=182, end=212, dist=2)]
[Match(start=60, end=90, dist=1), Match(start=182, end=212, dist=2)]
[Match(start=60, end=90, dist=1)]

I was very surprised, that when I increase the maximum distance, the number of matches is reduced and not increased. I tried to use find_near_matches_with_ngrams, but it gave the same result. Why is this happening? Maybe I'm doing something wrong? Thank you in advance!

[taleinat]

Hi Anna,

I'm happy fuzzysearch is useful for you!

Which version of fuzzysearch are you using? With the latest version, 0.2.2, find_near_matches(subseq, seq, 0) raises exception (as it should). Calling it with a limit for the maximum Levenshtein distance works and returns the expected results. This is done by passing max_l_dist=max_distance instead of just max_distance as a third parameter.

Here is my example interpreter session:

>>> import fuzzysearch
>>> fuzzysearch.__version__
'0.2.2'
>>> fuzzysearch.find_near_matches(subseq, seq, max_l_dist=4)
[Match(start=60, end=90, dist=1), Match(start=121, end=151, dist=2), Match(start=182, end=212, dist=2)]
>>> fuzzysearch.find_near_matches(subseq, seq, 3)
Traceback (most recent call last):
  File "<pyshell#12>", line 1, in <module>
    fuzzysearch.find_near_matches(subseq, seq, 3)
  File "C:\Python34\lib\site-packages\fuzzysearch\__init__.py", line 59, in find_near_matches
    raise ValueError('# insertions must be limited!')
ValueError: # insertions must be limited!

[AnnaNenarokova]

I have updated my fuzzysearch to 0.2.2, and everything works fine now. Thank you very much!

[taleinat]

Great!