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Merge branch 'py38-eol' of https://github.com/biocpy/iranges into py3…
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…8-eol
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@jkanche
jkanche committed Dec 8, 2024
2 parents ff1ade6 + 185e9c6 commit 2e9e7be
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Showing 2 changed files with 36 additions and 113 deletions.
140 changes: 34 additions & 106 deletions src/iranges/IRanges.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,11 +40,7 @@ def __iter__(self):

def __next__(self):
if self._current_index < len(self._iranges):
iter_row_index = (
self._iranges.names[self._current_index]
if self._iranges.names is not None
else None
)
iter_row_index = self._iranges.names[self._current_index] if self._iranges.names is not None else None

iter_slice = self._iranges.get_row(self._current_index)
self._current_index += 1
Expand Down Expand Up @@ -159,9 +155,7 @@ def _validate_mcols(self):
raise TypeError("'mcols' should be a BiocFrame")

if self._mcols.shape[0] != len(self._start):
raise ValueError(
"Number of rows in 'mcols' should be equal to length of 'start'"
)
raise ValueError("Number of rows in 'mcols' should be equal to length of 'start'")

def _sanitize_metadata(self, metadata):
if metadata is None:
Expand Down Expand Up @@ -315,9 +309,7 @@ def get_names(self) -> Optional[Names]:
"""
return self._names

def set_names(
self, names: Optional[Sequence[str]], in_place: bool = False
) -> "IRanges":
def set_names(self, names: Optional[Sequence[str]], in_place: bool = False) -> "IRanges":
"""
Args:
names:
Expand Down Expand Up @@ -373,9 +365,7 @@ def get_mcols(self) -> BiocFrame:
"""
return self._mcols

def set_mcols(
self, mcols: Optional[BiocFrame], in_place: bool = False
) -> "IRanges":
def set_mcols(self, mcols: Optional[BiocFrame], in_place: bool = False) -> "IRanges":
"""Set new metadata about ranges.
Args:
Expand Down Expand Up @@ -428,9 +418,7 @@ def get_metadata(self) -> dict:
"""
return self._metadata

def set_metadata(
self, metadata: Optional[dict], in_place: bool = False
) -> "IRanges":
def set_metadata(self, metadata: Optional[dict], in_place: bool = False) -> "IRanges":
"""Set or replace metadata.
Args:
Expand Down Expand Up @@ -490,9 +478,7 @@ def __len__(self) -> int:
"""
return len(self._start)

def __getitem__(
self, subset: Union[Sequence, int, str, bool, slice, range]
) -> "IRanges":
def __getitem__(self, subset: Union[Sequence, int, str, bool, slice, range]) -> "IRanges":
"""Subset the IRanges.
Args:
Expand All @@ -513,9 +499,7 @@ def __getitem__(
metadata=self._metadata,
)

def __setitem__(
self, args: Union[Sequence, int, str, bool, slice, range], value: "IRanges"
):
def __setitem__(self, args: Union[Sequence, int, str, bool, slice, range], value: "IRanges"):
"""Add or update positions (in-place operation).
Args:
Expand Down Expand Up @@ -619,9 +603,7 @@ def __str__(self) -> str:
data = self._mcols.column(col)
showed = show_as_cell(data, indices)
header = [col, "<" + ut.print_type(data) + ">"]
showed = ut.truncate_strings(
showed, width=max(40, len(header[0]), len(header[1]))
)
showed = ut.truncate_strings(showed, width=max(40, len(header[0]), len(header[1])))
if insert_ellipsis:
showed = showed[:3] + ["..."] + showed[3:]
columns.append(header + showed)
Expand Down Expand Up @@ -781,9 +763,7 @@ def clip_intervals(
_width = val.width[0]

_pshift = shift if isinstance(shift, int) else _ashift[counter]
_pwidth = (
width if width is None or isinstance(width, int) else _awidth[counter]
)
_pwidth = width if width is None or isinstance(width, int) else _awidth[counter]

if _pshift > 0:
_start += _pshift
Expand Down Expand Up @@ -953,9 +933,7 @@ def order(self, decreasing: bool = False) -> np.ndarray:
Returns:
NumPy vector containing index positions in the sorted order.
"""
order_buf = sorted(
range(len(self)), key=lambda i: (self._start[i], self._width[i])
)
order_buf = sorted(range(len(self)), key=lambda i: (self._start[i], self._width[i]))

if decreasing:
return np.asarray(order_buf[::-1])
Expand Down Expand Up @@ -1038,9 +1016,7 @@ def gaps(self, start: Optional[int] = None, end: Optional[int] = None) -> "IRang

return IRanges(_gapstarts, _gapends)

def gaps_numpy(
self, start: Optional[int] = None, end: Optional[int] = None
) -> "IRanges":
def gaps_numpy(self, start: Optional[int] = None, end: Optional[int] = None) -> "IRanges":
"""Gaps returns an ``IRanges`` object representing the set of integers that remain after the intervals are
removed specified by the start and end arguments.
Expand Down Expand Up @@ -1163,9 +1139,7 @@ def disjoin(self, with_reverse_map: bool = False) -> "IRanges":
#### intra range methods ####
#############################

def shift(
self, shift: Union[int, List[int], np.ndarray], in_place: bool = False
) -> "IRanges":
def shift(self, shift: Union[int, List[int], np.ndarray], in_place: bool = False) -> "IRanges":
"""Shifts all the intervals by the amount specified by the ``shift`` argument.
Args:
Expand Down Expand Up @@ -1225,23 +1199,15 @@ def narrow(
end = self._sanitize_vec_argument(end, allow_none=True)
width = self._sanitize_vec_argument(width, allow_none=True)

if (all(x is not None for x in (start, end, width))) or (
all(x is None for x in (start, end, width))
):
raise ValueError(
"Two out of three ('start', 'end' or 'width') arguments must be provided."
)
if (all(x is not None for x in (start, end, width))) or (all(x is None for x in (start, end, width))):
raise ValueError("Two out of three ('start', 'end' or 'width') arguments must be provided.")

if width is not None:
if (isinstance(width, int) and width < 0) or (
isinstance(width, np.ndarray) and any(x < 0 for x in width)
):
if (isinstance(width, int) and width < 0) or (isinstance(width, np.ndarray) and any(x < 0 for x in width)):
raise ValueError("'width' cannot be negative.")

if start is None and end is None:
raise ValueError(
"If 'width' is provided, either 'start' or 'end' must be provided."
)
raise ValueError("If 'width' is provided, either 'start' or 'end' must be provided.")

output = self._define_output(in_place)

Expand All @@ -1253,18 +1219,12 @@ def narrow(
_width = value.width[0]
_oend = value.end[0]

_pstart = (
start if start is None or isinstance(start, int) else start[counter]
)
_pwidth = (
width if width is None or isinstance(width, int) else width[counter]
)
_pstart = start if start is None or isinstance(start, int) else start[counter]
_pwidth = width if width is None or isinstance(width, int) else width[counter]
_pend = end if end is None or isinstance(end, int) else end[counter]

if _pend is not None and _pend > 0 and _pend > _width:
raise ValueError(
f"Provided 'end' is greater than width of the interval for: {counter}"
)
raise ValueError(f"Provided 'end' is greater than width of the interval for: {counter}")

if _pstart is not None:
if _pstart > 0:
Expand Down Expand Up @@ -1294,9 +1254,7 @@ def narrow(
_width = _width + _pend + 1

if _width < 0:
raise ValueError(
f"Provided 'start' or 'end' arguments lead to negative width for interval: {counter}."
)
raise ValueError(f"Provided 'start' or 'end' arguments lead to negative width for interval: {counter}.")

new_starts.append(_start)
new_widths.append(_width)
Expand All @@ -1310,9 +1268,7 @@ def narrow(
def resize(
self,
width: Union[int, List[int], np.ndarray],
fix: Union[
Literal["start", "end", "center"], List[Literal["start", "end", "center"]]
] = "start",
fix: Union[Literal["start", "end", "center"], List[Literal["start", "end", "center"]]] = "start",
in_place: bool = False,
) -> "IRanges":
"""Resize ranges to the specified ``width`` where either the ``start``, ``end``, or ``center`` is used as an
Expand Down Expand Up @@ -1380,14 +1336,10 @@ def resize(

output = self._define_output(in_place)
output._start = np.asarray(new_starts)
output._width = (
np.repeat(_awidth, len(self)) if isinstance(_awidth, int) else _awidth
)
output._width = np.repeat(_awidth, len(self)) if isinstance(_awidth, int) else _awidth
return output

def flank(
self, width: int, start: bool = True, both: bool = False, in_place: bool = False
) -> "IRanges":
def flank(self, width: int, start: bool = True, both: bool = False, in_place: bool = False) -> "IRanges":
"""Compute flanking ranges for each range. The logic is from the `IRanges` package.
If ``start`` is ``True`` for a given range, the flanking occurs at the `start`,
Expand Down Expand Up @@ -1460,9 +1412,7 @@ def flank(

return output

def promoters(
self, upstream: int = 2000, downstream: int = 200, in_place: bool = False
) -> "IRanges":
def promoters(self, upstream: int = 2000, downstream: int = 200, in_place: bool = False) -> "IRanges":
"""Extend intervals to promoter regions.
Generates promoter ranges relative to the transcription start site (TSS),
Expand Down Expand Up @@ -1585,9 +1535,7 @@ def restrict(

return IRanges(new_starts, new_widths, validate=False)

def overlap_indices(
self, start: Optional[int] = None, end: Optional[int] = None
) -> np.ndarray:
def overlap_indices(self, start: Optional[int] = None, end: Optional[int] = None) -> np.ndarray:
"""Find overlaps with the start and end positions.
Args:
Expand Down Expand Up @@ -1724,26 +1672,20 @@ def intersect_ncls(self, other: "IRanges", delete_index: bool = True) -> "IRange

other._build_ncls_index()

self_indexes, other_indexes = other._ncls.all_overlaps_both(
self.start, self.end, np.arange(len(self))
)
self_indexes, other_indexes = other._ncls.all_overlaps_both(self.start, self.end, np.arange(len(self)))

if delete_index:
other._delete_ncls_index()

self_new_starts = self.start[self_indexes]
other_new_starts = other.start[other_indexes]

new_starts = np.where(
self_new_starts > other_new_starts, self_new_starts, other_new_starts
)
new_starts = np.where(self_new_starts > other_new_starts, self_new_starts, other_new_starts)

self_new_ends = self.end[self_indexes]
other_new_ends = other.end[other_indexes]

new_ends = np.where(
self_new_ends < other_new_ends, self_new_ends, other_new_ends
)
new_ends = np.where(self_new_ends < other_new_ends, self_new_ends, other_new_ends)

return IRanges(new_starts, new_ends - new_starts).reduce()

Expand Down Expand Up @@ -1865,14 +1807,10 @@ def find_overlaps(
raise TypeError("'query' is not a `IRanges` object.")

if query_type not in ["any", "start", "end", "within"]:
raise ValueError(
f"'query_type' must be one of {', '.join(['any', 'start', 'end', 'within'])}."
)
raise ValueError(f"'query_type' must be one of {', '.join(['any', 'start', 'end', 'within'])}.")

if select not in ["all", "first", "last", "arbitrary"]:
raise ValueError(
f"'select' must be one of {', '.join(['all', 'first', 'last', 'arbitrary'])}."
)
raise ValueError(f"'select' must be one of {', '.join(['all', 'first', 'last', 'arbitrary'])}.")

_tgap = 0 if max_gap == -1 else max_gap

Expand Down Expand Up @@ -2032,14 +1970,8 @@ def _generic_search(
val.end[0] + (counter * step_end) + 1 > max_end + 1
and val.start[0] - (counter * step_start) - 1 < min_start - 1
)
or (
step_end == 0
and val.start[0] - (counter * step_start) - 1 < min_start - 1
)
or (
step_start == 0
and val.end[0] + (counter * step_end) + 1 > max_end + 1
)
or (step_end == 0 and val.start[0] - (counter * step_start) - 1 < min_start - 1)
or (step_start == 0 and val.end[0] + (counter * step_end) + 1 > max_end + 1)
):
_iterate = False
_hits = []
Expand Down Expand Up @@ -2082,9 +2014,7 @@ def nearest(
raise TypeError("`query` is not a `IRanges` object.")

if select not in ["all", "arbitrary"]:
raise ValueError(
f"'select' must be one of {', '.join(['all', 'arbitrary'])}."
)
raise ValueError(f"'select' must be one of {', '.join(['all', 'arbitrary'])}.")

hits = self._generic_search(query, 1, 1, 10000000, 1, select, delete_index)
self._delete_ncls_index()
Expand Down Expand Up @@ -2189,9 +2119,7 @@ def distance(self, query: "IRanges") -> np.ndarray:
for i in range(len(self)):
i_self = self[i]
i_query = query[i]
_gap, _overlap = calc_gap_and_overlap(
(i_self.start[0], i_self.end[0]), (i_query.start[0], i_query.end[0])
)
_gap, _overlap = calc_gap_and_overlap((i_self.start[0], i_self.end[0]), (i_query.start[0], i_query.end[0]))

distance = _gap
if _gap is None:
Expand Down
9 changes: 2 additions & 7 deletions src/iranges/interval.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -66,18 +66,13 @@ def create_np_interval_vector(
cov[_start:_end] += value

if with_reverse_map:
_ = [
revmap[x].append(name if name is not None else counter + 1)
for x in range(_start, _end)
]
_ = [revmap[x].append(name if name is not None else counter + 1) for x in range(_start, _end)]

counter += 1
return cov[1:], revmap


def calc_gap_and_overlap(
first: Tuple[int, int], second: Tuple[int, int]
) -> Tuple[Optional[int], Optional[int]]:
def calc_gap_and_overlap(first: Tuple[int, int], second: Tuple[int, int]) -> Tuple[Optional[int], Optional[int]]:
"""Calculate gap and/or overlap between two intervals.
Args:
Expand Down

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