move Defect and Strand class definitions out of Location class, small…

… fix in stockholm.fts2row()

sugar/_io/genbank.py

@@ -3,7 +3,8 @@
 `Genbank`_ reader
 """
 
-from sugar.core.seq import Attr, BioSeq, Meta, Feature, FeatureList, Location
+from sugar.core.fts import Defect, Feature, FeatureList, Location
+from sugar.core.seq import Attr, BioSeq, Meta
 from sugar._io.util import _add_fmt_doc
 
 
@@ -34,21 +35,21 @@ def _parse_locs(loc: str):
 
 
 def _parse_single_loc(loc: str):
-    defect = Location.Defect.NONE
+    defect = Defect.NONE
     if loc[0] == '<':
-        defect |= Location.Defect.BEYOND_LEFT
+        defect |= Defect.BEYOND_LEFT
         loc = loc[1:]
     if '>' in loc:
-        defect |= Location.Defect.BEYOND_RIGHT
+        defect |= Defect.BEYOND_RIGHT
         loc = loc.replace('>', '')
     if ".." in loc:
         splitter = ".."
     elif "." in loc:
         splitter = "."
-        defect |= Location.Defect.UNKNOWN_SINGLE_BETWEEN
+        defect |= Defect.UNKNOWN_SINGLE_BETWEEN
     elif "^" in loc:
         splitter = "^"
-        defect |= Location.Defect.BETWEEN_CONSECUTIVE
+        defect |= Defect.BETWEEN_CONSECUTIVE
     else:
         # single base
         return Location(int(loc)-1, int(loc), defect=defect)

sugar/_io/stockholm.py

@@ -20,7 +20,7 @@ def is_stockholm(f, **kw):
 
 def row2fts(row, type_=None, seqid=None):
     import re
-    from sugar.core.fts import Feature, FeatureList, Location
+    from sugar.core.fts import Defect, Feature, FeatureList, Location
     i = 0
     fts = []
     while i < len(row):
@@ -36,14 +36,14 @@ def row2fts(row, type_=None, seqid=None):
             name = names.pop()
             if i == 0 and row[0] != '|' and j == len(row):
                 assert row[-1] != '|'
-                defect = Location.Defect.MISS_LEFT | Location.Defect.MISS_RIGHT
+                defect = Defect.MISS_LEFT | Defect.MISS_RIGHT
             if i == 0 and row[0] != '|':
-                defect = Location.Defect.MISS_LEFT
+                defect = Defect.MISS_LEFT
             elif j == len(row):
                 assert row[-1] != '|'
-                defect = Location.Defect.MISS_RIGHT
+                defect = Defect.MISS_RIGHT
             else:
-                defect = Location.Defect.NONE
+                defect = Defect.NONE
             loc = Location(i, stop, defect=defect)
             ft = Feature(type_, [loc])
             ft.meta.name = name
@@ -79,9 +79,11 @@ def fts2row(fts):
         if l < len(name)-2:
             warn('Feature name too long, shorten it')
             rowp = '.' + name[:l-2] + '.'
-        if ft.loc.Defect.MISS_LEFT not in ft.loc.defect:
+        if (ft.loc.defect.MISS_LEFT not in ft.loc.defect and
+                ft.loc.defect.BEYOND_LEFT not in ft.loc.defect):
             rowp = '|' + rowp[1:]
-        if ft.loc.Defect.MISS_RIGHT not in ft.locs[-1].defect:
+        if (ft.loc.defect.MISS_RIGHT not in ft.locs[-1].defect and
+                ft.loc.defect.BEYOND_RIGHT not in ft.locs[-1].defect):
             rowp = rowp[:-1] + '|'
         assert len(rowp) == l
         row.append(rowp)

sugar/core/fts.py

@@ -1,7 +1,7 @@
 # (C) 2024, Tom Eulenfeld, MIT license
 
 """
-Feature related classes `.Feature`, `.FeatureList`, `.Location`, `.Location.Strand`, `.Location.Defect`
+Feature related classes `.Feature`, `.FeatureList`, `.Location`, `.Strand`, `.Defect`
 """
 
 # Originally, this file was based on the annotation module from the biotite package.
@@ -74,8 +74,6 @@ class Strand(StrEnum):
 
 
 class Location():
-    Strand = Strand
-    Defect = Defect
 
     def __init__(self, start, stop, strand='+', defect=0, meta=None):
         """
@@ -657,9 +655,9 @@ def slice(self, start, stop, rel=0):
                     # given location range
                     defect = loc.defect
                     if loc.start < start:
-                        defect |= Location.Defect.MISS_LEFT
+                        defect |= Defect.MISS_LEFT
                     if loc.stop > stop:
-                        defect |= Location.Defect.MISS_RIGHT
+                        defect |= Defect.MISS_RIGHT
                     lstart = max(start, loc.start) - rel
                     lstop = min(stop, loc.stop) - rel
                     locs_in_scope.append(Location(

sugar/tests/test_core_fts.py

@@ -73,8 +73,8 @@ def test_fts_slice():
     assert fts.slice(None, None) == fts
     fts2 = fts.slice(1, fts.loc_range[1]-1)
     assert len(fts2) == len(fts)
-    assert fts[0].loc.defect == fts2[0].loc.Defect.NONE
-    assert fts2[0].loc.defect == fts2[0].loc.Defect.MISS_LEFT | fts2[0].loc.Defect.MISS_RIGHT
+    assert fts[0].loc.defect == fts2[0].loc.defect.NONE
+    assert fts2[0].loc.defect == fts2[0].loc.defect.MISS_LEFT | fts2[0].loc.defect.MISS_RIGHT
 
 
 def test_ft_overlaps():

sugar/tests/test_core_seq.py

@@ -169,7 +169,7 @@ def test_seqs_getitem_special():
     assert seq2 == seq3
     assert len(seq2.fts) == 2
     assert all(len(ft) == 99 for ft in seq2.fts)
-    assert all(ft.loc.defect == ft.loc.Defect.MISS_LEFT | ft.loc.Defect.MISS_RIGHT for ft in seq2.fts)
+    assert all(ft.loc.defect == ft.loc.defect.MISS_LEFT | ft.loc.defect.MISS_RIGHT for ft in seq2.fts)
     seq2 = seq.sl(update_fts=True)['cds']
     assert seq2['cds'].data == seq['cds'].data
     assert len(seq2) == len(seq2['cds'])

sugar/tests/test_io_stockholm.py

@@ -48,10 +48,10 @@ def test_stockholm_row2fts2row():
     assert len(fts3) == 1
     assert fts1[0].name == '1'
     assert fts2[0].name == '1'
-    Defect = fts1[0].loc.Defect
-    assert fts1[0].loc.defect == Defect.MISS_LEFT
-    assert fts1[1].loc.defect == Defect.NONE
-    assert fts2[-1].loc.defect == Defect.MISS_RIGHT
+    defect = fts1[0].loc.defect
+    assert fts1[0].loc.defect == defect.MISS_LEFT
+    assert fts1[1].loc.defect == defect.NONE
+    assert fts2[-1].loc.defect == defect.MISS_RIGHT
     assert len(fts3[0]) == 1003
     row1b = fts2row(fts1)
     row2b = fts2row(fts2)