fast-ctc-decoder 0.3.9

Fast CTC decoding library.

fast-ctc-decoder

Blitzing fast CTC decoding library.

[!NOTE]
Note: compared to the original fast-ctc-decode project, this fork is renamed to fast-ctc-decoder and keeps only the Python/Rust extension build; the Node/WebAssembly build has been removed.

$ pip install fast-ctc-decoder

Usage

>>> from fast_ctc_decoder import beam_search, viterbi_search
>>>
>>> alphabet = "NACGT"
>>> posteriors = np.random.rand(100, len(alphabet)).astype(np.float32)
>>>
>>> seq, path = viterbi_search(posteriors, alphabet)
>>> seq
'ACACTCGCAGCGCGATACGACTGATCGAGATATACTCAGTGTACACAGT'
>>>
>>> seq, path = beam_search(posteriors, alphabet, beam_size=5, beam_cut_threshold=0.1)
>>> seq
'ACACTCGCAGCGCGATACGACTGATCGAGATATACTCAGTGTACACAGT'

Benchmark

Implementation	Time (s)	URL
Viterbi (Rust)	0.0003	ankandrew/fast-ctc-decoder
Viterbi (Python)	0.0022
Beam Search (Rust)	0.0033	ankandrew/fast-ctc-decoder
Beam Search (C++)	0.1034	parlance/ctcdecode
Beam Search (Python)	3.3337	githubharald/CTCDecoder

Developer Quickstart

Python

$ git clone https://github.com/ankandrew/fast-ctc-decoder.git
$ cd fast-ctc-decoder
$ pip install --user maturin
$ make test

Note: You'll need a recent rust compiler on your path to build the project.

By default, a fast (and less accurate) version of exponentiation is used for the 2D search. This can be disabled by passing --cargo-extra-args="--no-default-features" to maturin, which provides more accurate calculations but makes the 2D search take about twice as long.

Credits

The original 1D beam search implementation was developed by @usamec for deepnano-blitz.

The 2D beam search is based on @jordisr and @ihh work in their pair consensus decoding paper.

Licence and Copyright

(c) 2019 Oxford Nanopore Technologies Ltd.

fast-ctc-decoder is distributed under the terms of the MIT License. If a copy of the License was not distributed with this file, You can obtain one at https://github.com/ankandrew/fast-ctc-decoder/

This project is a fork of the original nanoporetech/fast-ctc-decode. This fork renames the package and removes the original Node/WebAssembly build.