fast-ctc-decoder
Blitzing fast CTC decoding library.
[!NOTE]
Note: compared to the originalfast-ctc-decodeproject, this fork is renamed tofast-ctc-decoderand 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.
1 maintainer
Metadata
1 maintainer
Release files for fast-ctc-decoder 0.3.9
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| fast_ctc_decoder-0.3.9.tar.gz | 29.0 kB | Details |
Built distributions (wheels)
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