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poke1024 / pyalign

Fast and Versatile Alignments for Python
MIT License
47 stars 6 forks source link

setup: add repo URL #4

Closed bertsky closed 1 year ago

bertsky commented 2 years ago

The project page on PyPI lacks a backref to Github due to this.

(Most images in the README do not render there, too.)

bertsky commented 2 years ago

(Most images in the README do not render there, too.)

should be fixed by 2nd commit

bertsky commented 2 years ago

Also, I wonder whether you'd want to mention https://github.com/maxbachmann/RapidFuzz as another fast (C++ based) versatile string alignment library for Python?

poke1024 commented 1 year ago

Not looked into details, but https://github.com/maxbachmann/RapidFuzz looks more like a string distance computation without any alignments.

bertsky commented 1 year ago

Not looked into details, but https://github.com/maxbachmann/RapidFuzz looks more like a string distance computation without any alignments.

It implement its own fast Needleman-Wunsch alignment (based on Hyyrö algorithm or Wagner-Fischer) in C++: https://github.com/maxbachmann/RapidFuzz/tree/main/src/rapidfuzz/distance, which then uses https://github.com/maxbachmann/rapidfuzz-cpp. (You can get the alignment result itself via .editops or .opcodes. But only the first-best.) Supports a fixed set of distance/similarity metrics. Includes semiglobal (prefix/postfix). No Smith-Waterman, though. And no custom weights.

No idea how it fits into your schema (how it scales time and memory wise, how well it utilises computing resources etc.) Just thought you might want to mention it in your elect list of other libraries.

poke1024 commented 1 year ago

OK, interesting, I added it to the README list in any case.