ikegami-yukino / shellinford-python Goto Github PK

I see the 0.3.2 release on PyPI, but running into trouble installing:

~ > pip install shellinford==0.3.2
Collecting shellinford==0.3.2
  Could not find a version that satisfies the requirement shellinford==0.3.2 (from versions: 0.3.1)
No matching distribution found for shellinford==0.3.2
~ > pip search shellinford
shellinford (0.3.2)  - Wavelet Matrix/Tree succinct data structure for full text
                       search (using shellinford C++ library)

Dear @ikegami-yukino,

I was wondering if there was a way to find maximal substring of query string given the FM index?

For example,

If the query is "IGPIVEGAGRE", and the FM Index contains "TIVEGAGRT", then it would return "IVEGAGR" and location (1)?

I am thinking this would involve building a bwt/fm index of both query and db and comparing, but not sure how to do this?
Thank you very much!

We're running into this error when reading a save FM index in Python 3 (it works well in Python 2!)

index_contains_kmer
    for _ in fm.search(kmer):
SystemError: <built-in function delete_MapIntInt> returned a result with an error set

Hello,
I am building the library with VC++2019 build tools and it crashes on a undefined identifier 'time' when compiling shellinford_fm_index.cc

Including to the source solved the problem

As you know, FM-index allows counting of occurrences of a pattern and finding the locations of these occurrences as separate operations. Because counting is very fast (while locating and extracting contents are not), it would be more reasonable to have "count", "locate" and "extract" as separate APIs.

Sorry for not creating PR. I'm not very knowledgeable to SWIG and etc.