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feat: Add GenBank file format support for biological sequence data #7951

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feat: Add GenBank file format support for biological sequence data #7951

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9097e80
feat: Add GenBank file format support for biological sequence data
behroozazarkhalili Jan 19, 2026
7d59f0a
style(genbank): use empty __init__.py to match other packaged modules
behroozazarkhalili Jan 19, 2026
f035611
refactor(genbank): split _parse_genbank into per-section helpers
behroozazarkhalili Jun 10, 2026
a4ead40
refactor(genbank): decode FEATURES via Json() type and declare static…
Jun 19, 2026
b5aa245
refactor(genbank): drop magic-byte decompression, rely on open()/xopen
Jul 3, 2026
cd55afa
docs(genbank): document the GenBank loader with a runnable example
Jul 3, 2026
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5 changes: 5 additions & 0 deletions src/datasets/packaged_modules/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
from .conll import conll
from .csv import csv
from .eval import eval
from .genbank import genbank
from .hdf5 import hdf5
from .iceberg import iceberg
from .imagefolder import imagefolder
Expand Down Expand Up @@ -63,6 +64,7 @@ def _hash_python_lines(lines: list[str]) -> str:
"lance": (lance.__name__, _hash_python_lines(inspect.getsource(lance).splitlines())),
"tsfile": (tsfile.__name__, _hash_python_lines(inspect.getsource(tsfile).splitlines())),
"iceberg": (iceberg.__name__, _hash_python_lines(inspect.getsource(iceberg).splitlines())),
"genbank": (genbank.__name__, _hash_python_lines(inspect.getsource(genbank).splitlines())),
}

# get importable module names and hash for caching
Expand Down Expand Up @@ -99,6 +101,9 @@ def _hash_python_lines(lines: list[str]) -> str:
".eval": ("eval", {}),
".lance": ("lance", {}),
".tsfile": ("tsfile", {}),
".gb": ("genbank", {}),
".gbk": ("genbank", {}),
".genbank": ("genbank", {}),
}
_EXTENSION_TO_MODULE.update({ext: ("imagefolder", {}) for ext in imagefolder.ImageFolder.EXTENSIONS})
_EXTENSION_TO_MODULE.update({ext.upper(): ("imagefolder", {}) for ext in imagefolder.ImageFolder.EXTENSIONS})
Expand Down
Empty file added src/datasets/packaged_modules/genbank/__init__.py
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