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791 type hints #792

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6a4595b
Add type hints to alignmentmapper.py
anju24 Sep 4, 2025
39185ab
Add type hints to assemblymapper.py
anju24 Sep 4, 2025
3441d0a
Add type hints to hgvs/edit.py
anju24 Sep 4, 2025
e5e9181
Add typehints to hgvsposition.py
anju24 Sep 4, 2025
0c236c7
Add type hints to files
anju24 Sep 4, 2025
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73 changes: 51 additions & 22 deletions src/hgvs/alignmentmapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,6 @@
# g. ... 123 124 125 126 127 128 129 130 131 132 133 ...
#


from bioutils.coordinates import strand_int_to_pm

import hgvs.location
Expand All @@ -41,15 +40,18 @@
from hgvs.utils import build_tx_cigar
from hgvs.utils.cigarmapper import CIGARMapper

from hgvs.dataproviders.interface import Interface
from hgvs.location import BaseOffsetInterval, Interval


def _zbc_to_hgvs(i):
def _zbc_to_hgvs(i: int) -> int:
"""Convert zero-based coordinate to hgvs (1 based, missing zero)"""
if i >= 0:
i += 1
return i


def _hgvs_to_zbc(i):
def _hgvs_to_zbc(i: int) -> int:
"""Convert hgvs (1 based, missing zero)"""
if i >= 1:
i -= 1
Expand Down Expand Up @@ -82,7 +84,9 @@ class AlignmentMapper:
"cigar_op",
)

def __init__(self, hdp, tx_ac, alt_ac, alt_aln_method):
def __init__(
self, hdp: Interface, tx_ac: str, alt_ac: str, alt_aln_method: str
) -> None:
self.tx_ac = tx_ac
self.alt_ac = alt_ac
self.alt_aln_method = alt_aln_method
Expand All @@ -108,11 +112,16 @@ def __init__(self, hdp, tx_ac, alt_ac, alt_aln_method):
# is that exons are adjacent. Assert that here.
sorted_tx_exons = sorted(tx_exons, key=lambda e: e["ord"])
for i in range(1, len(sorted_tx_exons)):
if sorted_tx_exons[i - 1]["tx_end_i"] != sorted_tx_exons[i]["tx_start_i"]:
if (
sorted_tx_exons[i - 1]["tx_end_i"]
!= sorted_tx_exons[i]["tx_start_i"]
):
raise HGVSDataNotAvailableError(
"AlignmentMapper(tx_ac={self.tx_ac}, "
"alt_ac={self.alt_ac}, alt_aln_method={self.alt_aln_method}): "
"Exons {a} and {b} are not adjacent".format(self=self, a=i, b=i + 1)
"Exons {a} and {b} are not adjacent".format(
self=self, a=i, b=i + 1
)
)

self.strand = tx_exons[0]["alt_strand"]
Expand All @@ -138,19 +147,21 @@ def __init__(self, hdp, tx_ac, alt_ac, alt_aln_method):
self.tgt_len = sum(tx_identity_info["lengths"])
self.cigarmapper = None

assert not (
(self.cds_start_i is None) ^ (self.cds_end_i is None)
), "CDS start and end must both be defined or neither defined"
assert not ((self.cds_start_i is None) ^ (self.cds_end_i is None)), (
"CDS start and end must both be defined or neither defined"
)

def __str__(self):
def __str__(self) -> str:
return (
"{self.__class__.__name__}: {self.tx_ac} ~ {self.alt_ac} ~ {self.alt_aln_method}; "
"{strand_pm} strand; offset={self.gc_offset}".format(
self=self, strand_pm=strand_int_to_pm(self.strand)
)
)

def g_to_n(self, g_interval, strict_bounds=None):
def g_to_n(
self, g_interval: Interval, strict_bounds: bool | None = None
) -> BaseOffsetInterval:
"""convert a genomic (g.) interval to a transcript cDNA (n.) interval"""

if strict_bounds is None:
Expand Down Expand Up @@ -183,7 +194,9 @@ def g_to_n(self, g_interval, strict_bounds=None):
uncertain=frs_cigar in "DI" or fre_cigar in "DI",
)

def n_to_g(self, n_interval, strict_bounds=None):
def n_to_g(
self, n_interval: BaseOffsetInterval, strict_bounds: bool | None = None
) -> Interval:
"""convert a transcript (n.) interval to a genomic (g.) interval"""

if strict_bounds is None:
Expand All @@ -210,12 +223,16 @@ def n_to_g(self, n_interval, strict_bounds=None):

# The returned interval would be uncertain when locating at alignment gaps
return hgvs.location.Interval(
start=hgvs.location.SimplePosition(gs, uncertain=n_interval.start.uncertain),
start=hgvs.location.SimplePosition(
gs, uncertain=n_interval.start.uncertain
),
end=hgvs.location.SimplePosition(ge, uncertain=n_interval.end.uncertain),
uncertain=grs_cigar in "DI" or gre_cigar in "DI",
)

def n_to_c(self, n_interval, strict_bounds=None):
def n_to_c(
self, n_interval: BaseOffsetInterval, strict_bounds: bool | None = None
) -> BaseOffsetInterval:
"""convert a transcript cDNA (n.) interval to a transcript CDS (c.) interval"""

if strict_bounds is None:
Expand All @@ -230,7 +247,9 @@ def n_to_c(self, n_interval, strict_bounds=None):
)
)

if strict_bounds and (n_interval.start.base <= 0 or n_interval.end.base > self.tgt_len):
if strict_bounds and (
n_interval.start.base <= 0 or n_interval.end.base > self.tgt_len
):
raise HGVSInvalidIntervalError(
"The given coordinate is outside the bounds of the reference sequence."
)
Expand All @@ -245,7 +264,9 @@ def pos_n_to_c(pos):
else:
c = pos.base - self.cds_end_i
c_datum = Datum.CDS_END
return hgvs.location.BaseOffsetPosition(base=c, offset=pos.offset, datum=c_datum)
return hgvs.location.BaseOffsetPosition(
base=c, offset=pos.offset, datum=c_datum
)

c_interval = hgvs.location.BaseOffsetInterval(
start=pos_n_to_c(n_interval.start),
Expand All @@ -254,7 +275,9 @@ def pos_n_to_c(pos):
)
return c_interval

def c_to_n(self, c_interval, strict_bounds=None):
def c_to_n(
self, c_interval: BaseOffsetInterval, strict_bounds: bool | None = None
) -> BaseOffsetInterval:
"""convert a transcript CDS (c.) interval to a transcript cDNA (n.) interval"""

if strict_bounds is None:
Expand All @@ -278,7 +301,9 @@ def pos_c_to_n(pos):
n -= 1
if n <= 0 or n > self.tgt_len:
if strict_bounds:
raise HGVSInvalidIntervalError(f"c.{pos} coordinate is out of bounds")
raise HGVSInvalidIntervalError(
f"c.{pos} coordinate is out of bounds"
)
return hgvs.location.BaseOffsetPosition(
base=n, offset=pos.offset, datum=Datum.SEQ_START
)
Expand All @@ -290,24 +315,28 @@ def pos_c_to_n(pos):
)
return n_interval

def g_to_c(self, g_interval, strict_bounds=None):
def g_to_c(
self, g_interval: Interval, strict_bounds: bool | None = None
) -> BaseOffsetInterval:
"""convert a genomic (g.) interval to a transcript CDS (c.) interval"""
return self.n_to_c(self.g_to_n(g_interval), strict_bounds=strict_bounds)

def c_to_g(self, c_interval, strict_bounds=None):
def c_to_g(
self, c_interval: BaseOffsetInterval, strict_bounds: bool | None = None
) -> Interval:
"""convert a transcript CDS (c.) interval to a genomic (g.) interval"""
return self.n_to_g(self.c_to_n(c_interval), strict_bounds=strict_bounds)

@property
def is_coding_transcript(self):
def is_coding_transcript(self) -> bool:
if (self.cds_start_i is not None) ^ (self.cds_end_i is not None):
raise HGVSError(
"{self.tx_ac}: CDS start_i and end_i"
" must be both defined or both undefined".format(self=self)
)
return self.cds_start_i is not None

def g_interval_is_inbounds(self, ival):
def g_interval_is_inbounds(self, ival: Interval) -> bool:
grs = ival.start.base - 1 - self.gc_offset
gre = ival.end.base - 1 - self.gc_offset
return grs >= 0 and gre <= self.cigarmapper.ref_len
Expand Down
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