rename some methods to be more consistent with sugars naming

anchorna/cli.py

@@ -234,7 +234,7 @@ def _cmd_view(fname_anchor, fname, mode='aa', align=None, score_use_fluke=None):
             anchor = anchors[int(align.lower().removeprefix('a'))]
             start = max(_apply_mode(fluke.start, fluke.offset, mode=mode) for fluke in anchor)
             for seq in seqs:
-                fluke = anchor.d[seq.id]
+                fluke = anchor.sid[seq.id]
                 seq.data = '-' * (start - _apply_mode(fluke.start, fluke.offset, mode=mode)) + seq.data
         seqs.write(fname_seq)
         subprocess.run(f'jalview {fname_seq} --features {fname_export}'.split())

anchorna/core.py

@@ -97,7 +97,7 @@ def anchor_at_pos(i, aas, w, gseqid, search_range,
         return
     words = {gword}
     todo = set(aas[1:].ids)
-    aas = aas.d
+    aas = aas.todict()
     toadd = []
     res = [(gscore, i, gseqid)]
     nfails = 0
@@ -270,7 +270,7 @@ def _split_cutout_pos(pos, mode, seqs, anchors, defaultB='^'):
         raise ValueError(f'{pos} only allowed in mode seq')
     A = pos
     if is_real_anchor := (A not in ('start', 'end', 'atg', '*')):
-        A = anchors[int(A.removeprefix('a'))].d
+        A = anchors[int(A.removeprefix('a'))].todict_seqid()
         if len(ids := set(A.keys()) - set(seqs.keys())) > 0:
             warn(f'Some anchor ids {ids} not present in sequences')
     return A, B, C, is_real_anchor

anchorna/util.py

@@ -68,15 +68,15 @@ def id(self):
     def __hash__(self):
         return hash((self.guide.start, self.guide.len, self.guide.offset))
 
-    def todict(self):
+    def todict_seqid(self):
         return {f.seqid: f for f in self}
 
     @property
-    def d(self):
-        return self.todict()
+    def sid(self):
+        return self.todict_seqid()
 
     @property
-    def ids(self):
+    def seqids(self):
         return [f.seqid for f in self]
 
     def tostr(self, i='', verbose=False, mode='aa'):
@@ -99,7 +99,7 @@ def key(f): return (False, '') if f.seqid == self.gseqid else (f.poor, f.seqid)
 
     @property
     def guide(self):
-        return self.d[self.gseqid]
+        return self.sid[self.gseqid]
 
     @property
     def minscore(self):
@@ -127,7 +127,7 @@ def nicely_overlaps_with(self, a2):
         a1 = self.good_flukes
         a2 = a2.good_flukes
         return (max(a1.guide.start, a2.guide.start) <= min(a1.guide.stop, a2.guide.stop) and
-                set(a1.ids) == set(a2.ids) and
+                set(a1.seqids) == set(a2.seqids) and
                 all((f1.start - f2.start == a1.guide.start - a2.guide.start and f1.poor == f2.poor) for f1, f2 in zip(a1.sort(), a2.sort())))
 
     def join_with(self, a2):