feat: blocks now store their position (not modulo length) along the path

2 files changed, 14 insertions, 13 deletions

diff --git a/pangraph/block.py b/pangraph/block.py
index 05b7806..e3953bd 100644
--- a/pangraph/block.py
+++ b/pangraph/block.py
@@ -26,6 +26,7 @@ class Block(object):
         super(Block, self).__init__()
         self.id   = randomid() if gen else 0
         self.seq  = None
+        self.pos  = {}
         self.muts = {}
 
     def __str__(self):
@@ -49,6 +50,10 @@ class Block(object):
     def isolates(self):
         return dict(Counter([k[0] for k in self.muts]))
 
+    @property
+    def positions(self):
+        return { tag:(pos, pos+self.len_of(*tag)) for tag, pos in self.pos.items() }
+
     # ------------------
     # static methods
 
@@ -56,6 +61,7 @@ class Block(object):
     def from_seq(cls, name, seq):
         new_blk      = cls()
         new_blk.seq  = as_array(seq)
+        new_blk.pos  = {(name, 0): 0}
         new_blk.muts = {(name, 0):{}}
 
         return new_blk
@@ -69,6 +75,7 @@ class Block(object):
         B      = Block()
         B.id   = d['id']
         B.seq  = as_array(d['seq'])
+        B.pos  = d['pos']
         B.muts = {unpack(k):v for k, v in d['muts'].items()}
 
         return B
@@ -222,6 +229,7 @@ class Block(object):
 
         return {'id'   : self.id,
                 'seq'  : "".join(str(n) for n in self.seq),
+                'pos'  : self.pos,
                 'muts' : {pack(k) : fix(v) for k, v in self.muts.items()}}
 
     def __len__(self):
@@ -233,6 +241,7 @@ class Block(object):
             start = val.start or 0
             stop  = val.stop or len(self.seq)
             b.seq = self.seq[start:stop]
+            b.pos = { iso : start+val.start for iso,start in self.pos.items() }
             for s, _ in self.muts.items():
                 b.muts[s] = {p-start:c for p,c in self.muts[s].items() if p>=start and p<stop}
             return b
diff --git a/pangraph/graph.py b/pangraph/graph.py
index bc1e9d9..70fd102 100644
--- a/pangraph/graph.py
+++ b/pangraph/graph.py
@@ -319,19 +319,11 @@ class Graph(object):
             or not accepted(hit):
                 continue
 
-            merged   = True
-            new_blks = self.merge(proc(hit))
+            merged = True
+            self.merge(proc(hit))
             merged_blks.add(hit['ref']['name'])
             merged_blks.add(hit['qry']['name'])
 
-            # for blk in new_blks:
-            #     for iso in blk.isolates:
-            #         path = self.seqs[iso]
-            #         x,  n  = path.position_of(blk)
-            #         lb, ub = max(0, x-EXTEND), min(x+blk.len_of(iso, n)+EXTEND, len(path))
-            #         subpath = path[lb:ub]
-            #         print(subpath, file=sys.stderr)
-            #         breakpoint("stop")
         self.remove_transitives()
 
         for path in self.seqs.values():
@@ -407,9 +399,6 @@ class Graph(object):
             # TODO: check that isos is constant along the chain
             for iso in self.blks[c[0][0]].isolates.keys():
                 self.seqs[iso].merge(c[0], c[-1], new_blk)
-                # for n in self.seqs[iso].nodes:
-                #     if n.blk.id in [e[0] for e in c]:
-                #         breakpoint("bad deletion")
 
             self.blks[new_blk.id] = new_blk
             for b, _ in c:
@@ -429,6 +418,9 @@ class Graph(object):
         # This is why in from_aln(aln) we set the start index to 0
         ref = old_ref[hit['ref']['start']:hit['ref']['end']]
         qry = old_qry[hit['qry']['start']:hit['qry']['end']]
+        print(ref.positions)
+        print(qry.positions)
+        breakpoint("test positions")
 
         if hit["orientation"] == Strand.Minus:
             qry = qry.rev_cmpl()