genomic-attribute-index Python bindings
The gai package wraps the Rust Genomic Attribute Index compressor, builder, and indexed reader.
It provides BGZF compression with a CSI built in the same pass, deterministic GAI construction,
TBI/CSI-backed exact, prefix, contains, or regex attribute queries, structured records and metadata,
and typed exceptions for stale or corrupt inputs.
from pathlib import Path
import gai
sorted_source = Path("annotations.sorted.gff3")
bgzf_source = Path("annotations.sorted.gff3.gz")
gai.compress(sorted_source, bgzf_source) # writes annotations.sorted.gff3.gz.csi
csi = Path("annotations.sorted.gff3.gz.csi")
gai.build_index(bgzf_source, csi, Path("annotations.sorted.gff3.gz.gai"), ["Name"])
records = gai.query_index(
bgzf_source, csi, Path("annotations.sorted.gff3.gz.gai"), "BRCA1"
)
prefix_records = gai.query_index(
bgzf_source, csi, Path("annotations.sorted.gff3.gz.gai"), "BRCA", match="prefix"
)
contains_records = gai.query_index(
bgzf_source, csi, Path("annotations.sorted.gff3.gz.gai"), "RCA", match="contains"
)
regex_records = gai.query_index(
bgzf_source, csi, Path("annotations.sorted.gff3.gz.gai"), r"^BRCA[0-9]+$", match="regex"
)
See the repository README for the complete API and development instructions.
1 maintainer
Metadata
1 maintainer
Release files for genomic-attribute-index 0.2.4
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
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| genomic_attribute_index-0.2.4.tar.gz | 135.8 kB | With provenance | Details for genomic_attribute_index-0.2.4.tar.gz |
Built distributions (wheels)
| File | Actions Reset | |||
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| genomic_attribute_index-0.2.4-cp310-abi3-win_amd64.whl | CPython 3.10 | abi3 | Windows x86-64 | Details for genomic_attribute_index-0.2.4-cp310-abi3-win_amd64.whl |
| genomic_attribute_index-0.2.4-cp310-abi3-manylinux_2_34_x86_64.whl | CPython 3.10 | abi3 | Linux glibc 2.34+ x86-64 | Details for genomic_attribute_index-0.2.4-cp310-abi3-manylinux_2_34_x86_64.whl |
| genomic_attribute_index-0.2.4-cp310-abi3-manylinux_2_34_aarch64.whl | CPython 3.10 | abi3 | Linux glibc 2.34+ ARM64 | Details for genomic_attribute_index-0.2.4-cp310-abi3-manylinux_2_34_aarch64.whl |
| genomic_attribute_index-0.2.4-cp310-abi3-macosx_11_0_arm64.whl | CPython 3.10 | abi3 | macOS 11.0+ ARM64 | Details for genomic_attribute_index-0.2.4-cp310-abi3-macosx_11_0_arm64.whl |
| genomic_attribute_index-0.2.4-cp310-abi3-macosx_10_12_x86_64.whl | CPython 3.10 | abi3 | macOS 10.12+ x86-64 | Details for genomic_attribute_index-0.2.4-cp310-abi3-macosx_10_12_x86_64.whl |
Total release size: 17.9 MB
Release files / genomic_attribute_index-0.2.4.tar.gz
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