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make parse_region 1-based #456

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make parse_region 1-based #456

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8 changes: 5 additions & 3 deletions src/cooler/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,7 @@ def parse_region_string(s: str) -> tuple[str, int | None, int | None]:
Parameters
----------
s : str
UCSC-style string, e.g. "chr5:10,100,000-30,000,000". Ensembl and FASTA
UCSC-style string, e.g. "chr5:10,100,001-30,000,000". Ensembl and FASTA
style sequence names are allowed. End coordinate must be greater than
or equal to start.

Expand Down Expand Up @@ -115,6 +115,9 @@ def _expect(tokens):
typ, token = next(tokens, (None, None))
_check_token(typ, token, ["COORD"])
start = parse_humanized(token)
if start == 0:
raise ValueError("Ranges are 1-based and hence cannot start at 0")
start -= 1

typ, token = next(tokens, (None, None))
_check_token(typ, token, ["HYPHEN"])
Expand Down Expand Up @@ -145,8 +148,7 @@ def parse_region(
chromsizes: dict | pd.Series | None = None
) -> GenomicRangeTuple:
"""
Genomic regions are represented as half-open intervals (0-based starts,
1-based ends) along the length coordinate of a contig/scaffold/chromosome.
Genomic regions are represented as half-open intervals along the length coordinate of a contig/scaffold/chromosome.

Parameters
----------
Expand Down
31 changes: 16 additions & 15 deletions tests/test_util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,26 +68,26 @@ def test_atoi():
def test_parse_region_string():
# UCSC-style names
assert util.parse_region_string("chr21") == ("chr21", None, None)
assert util.parse_region_string("chr21:1000-2000") == ("chr21", 1000, 2000)
assert util.parse_region_string("chr21:1,000-2,000") == ("chr21", 1000, 2000)
assert util.parse_region_string("chr21:1001-2000") == ("chr21", 1000, 2000)
assert util.parse_region_string("chr21:1,001-2,000") == ("chr21", 1000, 2000)

# Ensembl style names
assert util.parse_region_string("6") == ("6", None, None)
assert util.parse_region_string("6:1000-2000") == ("6", 1000, 2000)
assert util.parse_region_string("6:1,000-2,000") == ("6", 1000, 2000)
assert util.parse_region_string("6:1001-2000") == ("6", 1000, 2000)
assert util.parse_region_string("6:1,001-2,000") == ("6", 1000, 2000)

# FASTA style names
assert util.parse_region_string("gb|accession|locus") == (
"gb|accession|locus",
None,
None,
)
assert util.parse_region_string("gb|accession|locus:1000-2000") == (
assert util.parse_region_string("gb|accession|locus:1001-2000") == (
"gb|accession|locus",
1000,
2000,
)
assert util.parse_region_string("gb|accession|locus:1,000-2,000") == (
assert util.parse_region_string("gb|accession|locus:1,001-2,000") == (
"gb|accession|locus",
1000,
2000,
Expand All @@ -100,23 +100,24 @@ def test_parse_region_string():
None,
)
assert util.parse_region_string("GL000207.1") == ("GL000207.1", None, None)
assert util.parse_region_string("GL000207.1:1000-2000") == (
assert util.parse_region_string("GL000207.1:1001-2000") == (
"GL000207.1",
1000,
2000,
)

# Trailing dash
assert util.parse_region_string("chr21:1000-") == ("chr21", 1000, None)
assert util.parse_region_string("chr21:1001-") == ("chr21", 1000, None)

# Humanized units
assert util.parse_region_string("6:1kb-2kb") == ("6", 1000, 2000)
assert util.parse_region_string("6:1k-2000") == ("6", 1000, 2000)
assert util.parse_region_string("6:1kb-2M") == ("6", 1000, 2000000)
assert util.parse_region_string("6:1Gb-") == ("6", 1000000000, None)
assert util.parse_region_string("6:1kb-2kb") == ("6", 999, 2000)
assert util.parse_region_string("6:1k-2000") == ("6", 999, 2000)
assert util.parse_region_string("6:1kb-2M") == ("6", 999, 2000000)
assert util.parse_region_string("6:1Gb-") == ("6", 1000000000 - 1, None)

# Bad inputs
for region in [
"chr1:0-100", # coords start at 1
"chr1:2,000-1,000", # reverse selection
"chr1::1000-2000", # more than one colon
"chr1:1kb-2kDa", # unknown unit kDa
Expand All @@ -132,13 +133,13 @@ def test_parse_region_string():
def test_parse_region():
chromsizes = util.read_chromsizes(op.join(datadir, "toy.chrom.sizes"))
assert util.parse_region(("chr1", 0, 10)) == ("chr1", 0, 10)
assert util.parse_region("chr1:0-10") == ("chr1", 0, 10)
assert util.parse_region("chr1:0-", chromsizes) == ("chr1", 0, chromsizes["chr1"])
assert util.parse_region("chr1:1-10") == ("chr1", 0, 10)
assert util.parse_region("chr1:1-", chromsizes) == ("chr1", 0, chromsizes["chr1"])

# Don't accept undefined end unless chromsizes exists
# NOTE: parse_region_string works here
with pytest.raises(ValueError):
util.parse_region("chr1:0-")
util.parse_region("chr1:1-")

# catch end < start in non-string case
with pytest.raises(ValueError):
Expand Down