Use accessor methods to access seqnames

CHANGELOG.md

@@ -1,8 +1,11 @@
 # Changelog
 
-## Version 0.4.27
+## Version 0.4.27 - 0.4.28
 
 - Implement `subtract` method, add tests.
+- Use accessor methods to access properties especially `get_seqnames()`
+- Modify search and overlap methods for strand-awareness.
+- Update tests and documentation.
 
 ## Version 0.4.26
 

src/genomicranges/GenomicRanges.py

@@ -208,7 +208,9 @@ def __init__(
             )
 
     def _build_reverse_seqindex(self, seqinfo: SeqInfo):
-        self._reverse_seqindex = ut.reverse_index.build_reverse_index(seqinfo.seqnames)
+        self._reverse_seqindex = ut.reverse_index.build_reverse_index(
+            seqinfo.get_seqnames()
+        )
 
     def _remove_reverse_seqindex(self):
         del self._reverse_seqindex
@@ -354,7 +356,7 @@ def __str__(self) -> str:
             header = ["seqnames", "<str>"]
             _seqnames = []
             for x in self._seqnames[indices]:
-                _seqnames.append(self._seqinfo.seqnames[x])
+                _seqnames.append(self._seqinfo.get_seqnames()[x])
 
             showed = _seqnames
             if insert_ellipsis:
@@ -407,7 +409,7 @@ def __str__(self) -> str:
                 + str(len(self._seqinfo))
                 + " sequences): "
                 + ut.print_truncated_list(
-                    self._seqinfo.seqnames,
+                    self._seqinfo.get_seqnames(),
                     sep=" ",
                     include_brackets=False,
                     transform=lambda y: y,
@@ -453,9 +455,9 @@ def get_seqnames(
         """
 
         if as_type == "factor":
-            return self._seqnames, self._seqinfo.seqnames
+            return self._seqnames, self._seqinfo.get_seqnames()
         elif as_type == "list":
-            return [self._seqinfo.seqnames[x] for x in self._seqnames]
+            return [self._seqinfo.get_seqnames()[x] for x in self._seqnames]
         else:
             raise ValueError("Argument 'as_type' must be 'factor' or 'list'.")
 
@@ -481,7 +483,7 @@ def set_seqnames(
 
         if not isinstance(seqnames, np.ndarray):
             seqnames = np.asarray(
-                [self._seqinfo.seqnames.index(x) for x in list(seqnames)]
+                [self._seqinfo.get_seqnames().index(x) for x in list(seqnames)]
             )
 
         output = self._define_output(in_place)
@@ -570,7 +572,7 @@ def get_strand(
                  vector is retuned.
 
                 If ``factor``, a tuple width levels as a dictionary and
-                  indices to ``seqinfo.seqnames`` is returned.
+                  indices to ``seqinfo.get_seqnames()`` is returned.
 
                 If ``list``, then codes are mapped to levels and returned.
 
@@ -1684,7 +1686,7 @@ def range(
         rev_map = []
         groups = []
 
-        for seq in self._seqinfo.seqnames:
+        for seq in self._seqinfo.get_seqnames():
             _iter_strands = [0] if ignore_strand is True else [1, -1, 0]
             for strd in _iter_strands:
                 _key = f"{seq}{_granges_delim}{strd}"
@@ -1738,7 +1740,7 @@ def gaps(
         all_grp_ranges = []
         groups = []
 
-        for i, chrm in enumerate(self._seqinfo.seqnames):
+        for i, chrm in enumerate(self._seqinfo.get_seqnames()):
             _iter_strands = [0] if ignore_strand is True else [1, -1, 0]
             for strd in _iter_strands:
                 _key = f"{chrm}{_granges_delim}{strd}"
@@ -1801,7 +1803,7 @@ def disjoin(
         rev_map = []
         groups = []
 
-        for seq in self._seqinfo.seqnames:
+        for seq in self._seqinfo.get_seqnames():
             _iter_strands = [0] if ignore_strand is True else [1, -1, 0]
             for strd in _iter_strands:
                 _key = f"{seq}{_granges_delim}{strd}"
@@ -1930,7 +1932,7 @@ def setdiff(self, other: "GenomicRanges") -> "GenomicRanges":
         range_bounds = all_combined.range(ignore_strand=True)
         rb_ends = {}
         for _, val in range_bounds:
-            rb_ends[val.seqnames[0]] = val.end[0]
+            rb_ends[val.get_seqnames()[0]] = val.end[0]
 
         x_gaps = self.gaps(end=rb_ends)
         x_gaps_u = x_gaps.union(other)
@@ -1960,7 +1962,7 @@ def intersect(self, other: "GenomicRanges") -> "GenomicRanges":
         range_bounds = all_combined.range(ignore_strand=True)
         rb_ends = {}
         for _, val in range_bounds:
-            rb_ends[val.seqnames[0]] = val.end[0]
+            rb_ends[val.get_seqnames()[0]] = val.end[0]
 
         _gaps = other.gaps(end=rb_ends)
         # _inter = self.setdiff(_gaps)
@@ -2098,8 +2100,26 @@ def find_overlaps(
         query_chrm_grps = query._group_indices_by_chrm(ignore_strand=ignore_strand)
 
         for group, indices in query_chrm_grps.items():
+            _subset = []
             if group in subject_chrm_grps:
-                _sub_subset = self[subject_chrm_grps[group]]
+                _subset.extend(subject_chrm_grps[group])
+
+            _grp_split = group.split(_granges_delim)
+            if _grp_split[1] != "0":
+                _any_grp_fwd = f"{_grp_split[0]}{_granges_delim}0"
+                if _any_grp_fwd in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_fwd])
+            else:
+                _any_grp_fwd = f"{_grp_split[0]}{_granges_delim}1"
+                if _any_grp_fwd in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_fwd])
+
+                _any_grp_rev = f"{_grp_split[0]}{_granges_delim}-1"
+                if _any_grp_rev in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_rev])
+
+            if len(_subset) > 0:
+                _sub_subset = self[_subset]
                 _query_subset = query[indices]
 
                 res_idx = _sub_subset._ranges.find_overlaps(
@@ -2112,7 +2132,7 @@ def find_overlaps(
                 )
 
                 for j, val in enumerate(res_idx):
-                    _rev_map = [subject_chrm_grps[group][x] for x in val]
+                    _rev_map = [_subset[x] for x in val]
                     rev_map[indices[j]] = _rev_map
 
         return rev_map
@@ -2172,8 +2192,26 @@ def count_overlaps(
         query_chrm_grps = query._group_indices_by_chrm(ignore_strand=ignore_strand)
 
         for group, indices in query_chrm_grps.items():
+            _subset = []
             if group in subject_chrm_grps:
-                _sub_subset = self[subject_chrm_grps[group]]
+                _subset.extend(subject_chrm_grps[group])
+
+            _grp_split = group.split(_granges_delim)
+            if _grp_split[1] != "0":
+                _any_grp_fwd = f"{_grp_split[0]}{_granges_delim}0"
+                if _any_grp_fwd in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_fwd])
+            else:
+                _any_grp_fwd = f"{_grp_split[0]}{_granges_delim}1"
+                if _any_grp_fwd in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_fwd])
+
+                _any_grp_rev = f"{_grp_split[0]}{_granges_delim}-1"
+                if _any_grp_rev in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_rev])
+
+            if len(_subset) > 0:
+                _sub_subset = self[_subset]
                 _query_subset = query[indices]
 
                 res_idx = _sub_subset._ranges.find_overlaps(
@@ -2186,7 +2224,7 @@ def count_overlaps(
                 )
 
                 for j, val in enumerate(res_idx):
-                    _rev_map = [subject_chrm_grps[group][x] for x in val]
+                    _rev_map = [_subset[x] for x in val]
                     rev_map[indices[j]] = len(_rev_map)
 
         return rev_map
@@ -2246,8 +2284,26 @@ def subset_by_overlaps(
         query_chrm_grps = query._group_indices_by_chrm(ignore_strand=ignore_strand)
 
         for group, indices in query_chrm_grps.items():
+            _subset = []
             if group in subject_chrm_grps:
-                _sub_subset = self[subject_chrm_grps[group]]
+                _subset.extend(subject_chrm_grps[group])
+
+            _grp_split = group.split(_granges_delim)
+            if _grp_split[1] != "0":
+                _any_grp_fwd = f"{_grp_split[0]}{_granges_delim}0"
+                if _any_grp_fwd in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_fwd])
+            else:
+                _any_grp_fwd = f"{_grp_split[0]}{_granges_delim}1"
+                if _any_grp_fwd in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_fwd])
+
+                _any_grp_rev = f"{_grp_split[0]}{_granges_delim}-1"
+                if _any_grp_rev in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_rev])
+
+            if len(_subset) > 0:
+                _sub_subset = self[_subset]
                 _query_subset = query[indices]
 
                 res_idx = _sub_subset._ranges.find_overlaps(
@@ -2260,7 +2316,7 @@ def subset_by_overlaps(
                 )
 
                 for _, val in enumerate(res_idx):
-                    _rev_map = [subject_chrm_grps[group][x] for x in val]
+                    _rev_map = [_subset[x] for x in val]
                     rev_map.extend(_rev_map)
 
         return self[list(set(rev_map))]
@@ -2300,16 +2356,34 @@ def nearest(
         query_chrm_grps = query._group_indices_by_chrm(ignore_strand=ignore_strand)
 
         for group, indices in query_chrm_grps.items():
+            _subset = []
             if group in subject_chrm_grps:
-                _sub_subset = self[subject_chrm_grps[group]]
+                _subset.extend(subject_chrm_grps[group])
+
+            _grp_split = group.split(_granges_delim)
+            if _grp_split[1] != "0":
+                _any_grp_fwd = f"{_grp_split[0]}{_granges_delim}0"
+                if _any_grp_fwd in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_fwd])
+            else:
+                _any_grp_fwd = f"{_grp_split[0]}{_granges_delim}1"
+                if _any_grp_fwd in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_fwd])
+
+                _any_grp_rev = f"{_grp_split[0]}{_granges_delim}-1"
+                if _any_grp_rev in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_rev])
+
+            if len(_subset) > 0:
+                _sub_subset = self[_subset]
                 _query_subset = query[indices]
 
                 res_idx = _sub_subset._ranges.nearest(
                     query=_query_subset._ranges, select=select, delete_index=False
                 )
 
                 for j, val in enumerate(res_idx):
-                    _rev_map = [subject_chrm_grps[group][x] for x in val]
+                    _rev_map = [_subset[x] for x in val]
                     rev_map[indices[j]] = _rev_map
 
         return rev_map
@@ -2345,16 +2419,34 @@ def precede(
         query_chrm_grps = query._group_indices_by_chrm(ignore_strand=ignore_strand)
 
         for group, indices in query_chrm_grps.items():
+            _subset = []
             if group in subject_chrm_grps:
-                _sub_subset = self[subject_chrm_grps[group]]
+                _subset.extend(subject_chrm_grps[group])
+
+            _grp_split = group.split(_granges_delim)
+            if _grp_split[1] != "0":
+                _any_grp_fwd = f"{_grp_split[0]}{_granges_delim}0"
+                if _any_grp_fwd in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_fwd])
+            else:
+                _any_grp_fwd = f"{_grp_split[0]}{_granges_delim}1"
+                if _any_grp_fwd in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_fwd])
+
+                _any_grp_rev = f"{_grp_split[0]}{_granges_delim}-1"
+                if _any_grp_rev in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_rev])
+
+            if len(_subset) > 0:
+                _sub_subset = self[_subset]
                 _query_subset = query[indices]
 
                 res_idx = _sub_subset._ranges.precede(
                     query=_query_subset._ranges, select=select, delete_index=False
                 )
 
                 for j, val in enumerate(res_idx):
-                    _rev_map = [subject_chrm_grps[group][x] for x in val]
+                    _rev_map = [_subset[x] for x in val]
                     rev_map[indices[j]] = _rev_map
 
         return rev_map
@@ -2390,16 +2482,34 @@ def follow(
         query_chrm_grps = query._group_indices_by_chrm(ignore_strand=ignore_strand)
 
         for group, indices in query_chrm_grps.items():
+            _subset = []
             if group in subject_chrm_grps:
-                _sub_subset = self[subject_chrm_grps[group]]
+                _subset.extend(subject_chrm_grps[group])
+
+            _grp_split = group.split(_granges_delim)
+            if _grp_split[1] != "0":
+                _any_grp_fwd = f"{_grp_split[0]}{_granges_delim}0"
+                if _any_grp_fwd in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_fwd])
+            else:
+                _any_grp_fwd = f"{_grp_split[0]}{_granges_delim}1"
+                if _any_grp_fwd in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_fwd])
+
+                _any_grp_rev = f"{_grp_split[0]}{_granges_delim}-1"
+                if _any_grp_rev in subject_chrm_grps:
+                    _subset.extend(subject_chrm_grps[_any_grp_rev])
+
+            if len(_subset) > 0:
+                _sub_subset = self[_subset]
                 _query_subset = query[indices]
 
                 res_idx = _sub_subset._ranges.follow(
                     query=_query_subset._ranges, select=select, delete_index=False
                 )
 
                 for j, val in enumerate(res_idx):
-                    _rev_map = [subject_chrm_grps[group][x] for x in val]
+                    _rev_map = [_subset[x] for x in val]
                     rev_map[indices[j]] = _rev_map
 
         return rev_map
@@ -2452,9 +2562,9 @@ def match(self, query: "GenomicRanges") -> List[List[int]]:
 
         for i in range(len(query)):
             try:
-                _seqname = query.seqnames[i]
+                _seqname = query.get_seqnames()[i]
             except Exception as _:
-                warn(f"'{query.seqnames[i]}' is not present in subject.")
+                warn(f"'{query.get_seqnames()[i]}' is not present in subject.")
 
             _strand = query._strand[i]
 
@@ -2653,7 +2763,7 @@ def tile_by_range(
                 val._ranges._start[0], val._ranges.end[0] - 1, twidth
             )
 
-            seqnames.extend([val.seqnames[0]] * len(all_intervals))
+            seqnames.extend([val.get_seqnames()[0]] * len(all_intervals))
             strand.extend([int(val.strand[0])] * len(all_intervals))
             starts.extend([x[0] for x in all_intervals])
             widths.extend(x[1] for x in all_intervals)
@@ -2715,7 +2825,7 @@ def tile(
                 val._ranges._start[0], val._ranges.end[0] - 1, twidth
             )
 
-            seqnames.extend([val.seqnames[0]] * len(all_intervals))
+            seqnames.extend([val.get_seqnames()[0]] * len(all_intervals))
             strand.extend([int(val.strand[0])] * len(all_intervals))
             starts.extend([x[0] for x in all_intervals])
             widths.extend(x[1] for x in all_intervals)
@@ -2757,7 +2867,7 @@ def sliding_windows(self, width: int, step: int = 1) -> "GenomicRanges":
                 step=step,
             )
 
-            seqnames.extend([val.seqnames[0]] * len(all_intervals))
+            seqnames.extend([val.get_seqnames()[0]] * len(all_intervals))
             strand.extend([int(val.strand[0])] * len(all_intervals))
             starts.extend([x[0] for x in all_intervals])
             widths.extend(x[1] for x in all_intervals)
@@ -2814,7 +2924,7 @@ def tile_genome(
 
         seqlen_ = seqlengths
         if isinstance(seqlengths, SeqInfo):
-            seqlen_ = dict(zip(seqlengths.seqnames, seqlengths.seqlengths))
+            seqlen_ = dict(zip(seqlengths.get_seqnames(), seqlengths.seqlengths))
 
         seqnames = []
         strand = []

src/genomicranges/SeqInfo.py

@@ -65,7 +65,7 @@ def __iter__(self):
 
     def __next__(self):
         if self._current_index < len(self._sinfo):
-            iter_row_index = self._sinfo.seqnames[self._current_index]
+            iter_row_index = self._sinfo._seqnames[self._current_index]
 
             iter_slice = self._sinfo[self._current_index]
             self._current_index += 1