From 37df6f21935f8087bc24641f5d338c7c97bd1e79 Mon Sep 17 00:00:00 2001 From: Jayaram Kancherla Date: Fri, 31 Jan 2025 16:03:53 -0800 Subject: [PATCH] Use the factor class to extract codes for seqnames (#6) --- setup.cfg | 2 +- src/dolomite_ranges/save_genomic_ranges.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/setup.cfg b/setup.cfg index b54a70e..50aa1a5 100644 --- a/setup.cfg +++ b/setup.cfg @@ -50,7 +50,7 @@ python_requires = >=3.9 install_requires = importlib-metadata; python_version<"3.8" dolomite-base>=0.4.2 - genomicranges>=0.4.10 + genomicranges>=0.6.1 biocframe>=0.5.8 h5py diff --git a/src/dolomite_ranges/save_genomic_ranges.py b/src/dolomite_ranges/save_genomic_ranges.py index 0447926..586bd79 100644 --- a/src/dolomite_ranges/save_genomic_ranges.py +++ b/src/dolomite_ranges/save_genomic_ranges.py @@ -47,9 +47,9 @@ def save_genomic_ranges( with h5py.File(os.path.join(path, "ranges.h5"), "w") as handle: ghandle = handle.create_group("genomic_ranges") - _seqnames, _ = x.get_seqnames(as_type="factor") + _seqnames = x.get_seqnames(as_type="factor") dl.write_integer_vector_to_hdf5( - ghandle, name="sequence", h5type="u4", x=_seqnames + ghandle, name="sequence", h5type="u4", x=_seqnames.get_codes() ) _ranges = x.get_ranges()