Dogma Data
Dogma Data is a Python package built for fast and efficient parsing of FASTA files, optimized for high-performance computing. It leverages multi-threading to fully utilize all available system threads, enabling parallel processing. Additionally, the package supports exporting parsed data to the HDF5 file format for easy storage and access.
Installation
To install Dogma Data, you can use pip:
pip install dogma-data
Usage
import dogma_data
vocab = {
'a': 0,
'g': 1,
'c': 2,
't': 3,
...
}
mapping = dogma_data.FastaMapping(vocab, vocab['a'])
(tokens, sequences, (taxons)) = dogma_data.parse_fasta('input_path.fa', dogma_data.HeaderType.TaxonId, mapping)
header_info = {"taxons": taxons}
dogma_data.export_hdf5(
'output_path.h5',
dogma_data.Splitter(
train_prop=0.95,
val_prop=0.025,
test_prop=0.025,
length=len(sequences) - 1,
),
tokens,
sequences,
header_info,
mapping
)
Requirements
- Python 3.10
License
This project is licensed under the MIT License - see the LICENSE file for details.
Contact
For any questions, feel free to reach out:
- Marcel Rød - roed@stanford.edu
- Miha Krajnc - miha.krajnc@cs.stanford.edu
1 maintainer
Metadata
1 maintainer
Release files for dogma-data 0.2.19
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Built distributions (wheels)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| dogma_data-0.2.19-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.12 | CPython 3.12 | Linux glibc 2.17+ x86-64 | Details for dogma_data-0.2.19-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
| dogma_data-0.2.19-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.11 | CPython 3.11 | Linux glibc 2.17+ x86-64 | Details for dogma_data-0.2.19-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
| dogma_data-0.2.19-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.10 | CPython 3.10 | Linux glibc 2.17+ x86-64 | Details for dogma_data-0.2.19-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
Total release size: 1.5 MB
Release files / dogma_data-0.2.19-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | dogma_data-0.2.19-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 498.0 kB |
| Tags | CPython 3.12 Linux glibc 2.17+ x86-64 |
|
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| Download URL | dogma_data-0.2.19-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 498.7 kB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 |
|
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| Size | 498.9 kB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
|
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