Make get_chromosomes species-agnostic with optional genome parameter#185
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LiudengZhang wants to merge 1 commit intoGenentech:mainfrom
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Make get_chromosomes species-agnostic with optional genome parameter#185LiudengZhang wants to merge 1 commit intoGenentech:mainfrom
LiudengZhang wants to merge 1 commit intoGenentech:mainfrom
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Add an optional genome parameter to get_chromosomes() so that shortcut names like "autosomes" resolve to the actual chromosomes in the genome (e.g. chr1-chr19 for mouse) instead of hardcoded human chr1-chr22. When no genome is provided, the function falls back to the existing human defaults for backward compatibility. Updated the two call sites in preprocess.py that already have genome objects (get_gc_matched_intervals, make_insertion_bigwig) to pass the genome through. Closes Genentech#167
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Closes #167.
get_chromosomes("autosomes")currently returns hardcoded human chromosomes (chr1-chr22), which is incorrect for other species (e.g. mouse only has chr1-chr19).This adds an optional
genomeparameter. When provided, chromosome names are read from the genome's sizes file and filtered by pattern (chr\d+for autosomes), so the function works correctly for any species. When omitted, it falls back to the existing human defaults for backward compatibility.Updated the two call sites in
preprocess.pythat already have genome objects loaded (get_gc_matched_intervals,make_insertion_bigwig) to pass the genome through.Tests added:
test_get_chromosomes_with_genome: uses a fake mouse genome (chr1-19 + chrX/Y/M) to verify all three shortcuts resolve correctly