fix: bug associated to position of using index absolutely instead of relative to true dictionary key

2 files changed, 8 insertions, 9 deletions

diff --git a/pangraph/graph.py b/pangraph/graph.py
index 2926d3f..afff779 100644
--- a/pangraph/graph.py
+++ b/pangraph/graph.py
@@ -478,7 +478,10 @@ class Graph(object):
                 blk_list.intersection_update(set([b.id for b in blks]))
 
         for tag in qry.muts.keys():
-            pos  = sorted([self.seqs[tag[0]].position_of(b, tag[1]) for b in new_qrys], key=lambda x: x[0])
+            try:
+                pos  = sorted([self.seqs[tag[0]].position_of(b, tag[1]) for b in new_qrys], key=lambda x: x[0])
+            except:
+                breakpoint("bad find")
             beg, end  = pos[0], pos[-1]
             blks = self.seqs[tag[0]][beg[0]-EXTEND:end[1]+EXTEND]
             blk_list.intersection_update(set([b.id for b in blks]))
diff --git a/pangraph/sequence.py b/pangraph/sequence.py
index dd9677b..6b9baba 100644
--- a/pangraph/sequence.py
+++ b/pangraph/sequence.py
@@ -88,12 +88,6 @@ class Path(object):
 
         return seq
 
-    # def position_of(self, blk):
-    #     for i, n in enumerate(self.nodes):
-    #         if n.blk == blk:
-    #             return i, n.num
-    #     raise ValueError("block not found in path")
-
     def rm_nil_blks(self):
         good, popped = [], set()
         for i, n in enumerate(self.nodes):
@@ -121,6 +115,8 @@ class Path(object):
             try:
                 i, j = ids.index(start[0]), ids.index(stop[0])
 
+                if N > 0:
+                    breakpoint("HIT")
                 if self.nodes[i].strand == start[1]:
                     beg, end, s = i, j, Strand.Plus
                 else:
@@ -154,8 +150,8 @@ class Path(object):
         self.position = np.cumsum([0] + [n.length(self.name) for n in self.nodes])
 
     def position_of(self, blk, num):
-        index = [i for i, n in enumerate(self.nodes) if n.blk == blk]
-        if len(index) <= num:
+        index = { n.num:i for i, n in enumerate(self.nodes) if n.blk == blk }
+        if not num in index:
             return None
         return (self.position[index[num]], self.position[index[num]+1])