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Use IntegerList and BooleanList for seqinfo's attributes #149

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Merged
merged 4 commits into from
Mar 22, 2025
Merged

Use IntegerList and BooleanList for seqinfo's attributes #149

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839b0fe
Use IntegerList and BooleanList for seqinfo's attributes
jkanche Mar 22, 2025
92dff75
keep them as lists
jkanche Mar 22, 2025
1caf279
update tests
jkanche Mar 22, 2025
3ce981b
revert some changes in tests
jkanche Mar 22, 2025
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8 changes: 4 additions & 4 deletions src/genomicranges/SeqInfo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ def _validate_seqnames(seqnames):


def _validate_seqlengths(seqlengths, num_seqs):
if not ut.is_list_of_type(seqlengths, int, ignore_none=True):
if not (isinstance(seqlengths, ut.IntegerList) or ut.is_list_of_type(seqlengths, int, ignore_none=True)):
raise ValueError("'seqlengths' should be a list of integers.")

if num_seqs != len(seqlengths):
Expand All @@ -32,7 +32,7 @@ def _validate_seqlengths(seqlengths, num_seqs):


def _validate_is_circular(is_circular, num_seqs):
if not ut.is_list_of_type(is_circular, bool, ignore_none=True):
if not (isinstance(is_circular, ut.BooleanList) or ut.is_list_of_type(is_circular, bool, ignore_none=True)):
raise ValueError("'is_circular' should be a list of booleans.")

if num_seqs != len(is_circular):
Expand Down Expand Up @@ -141,8 +141,8 @@ def __init__(
"""
self._seqnames = list(seqnames)
self._reverse_seqnames = None
self._seqlengths = self._flatten_incoming(seqlengths, int)
self._is_circular = self._flatten_incoming(is_circular, bool)
self._seqlengths = list(ut.IntegerList(self._flatten_incoming(seqlengths, int)))
self._is_circular = list(ut.BooleanList(self._flatten_incoming(is_circular, bool)))
self._genome = self._flatten_incoming(genome, str)

if validate:
Expand Down
12 changes: 11 additions & 1 deletion tests/test_SeqInfo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,7 @@ def test_subset_seqinfo():

assert isinstance(subset, SeqInfo)
assert subset.seqnames == ["chr2", "chr3"]
assert subset.seqlengths == [101, 102]
assert list(subset.seqlengths) == [101, 102]


def test_merge_SeqInfo():
Expand Down Expand Up @@ -160,3 +160,13 @@ def test_copy_SeqInfo():

deepcopy_seq = deepcopy(seq)
assert seq.seqnames == deepcopy_seq.seqnames


def test_seqlength_types():
s = SeqInfo(["A"], seqlengths=[np.uint64(100)])

assert isinstance(s, SeqInfo)
assert list(s._seqlengths) == [100]

s = SeqInfo(seqnames=["A"], seqlengths=[100], is_circular=[None], genome=[None])
assert isinstance(s, SeqInfo)