Merge branch 'feat/fasta-parser' into feat/anchor-matching

4 files changed, 6 insertions, 6 deletions

diff --git a/Makefile b/Makefile
index ab398b6..0fe7c0a 100644
--- a/Makefile
+++ b/Makefile
@@ -55,7 +55,7 @@ staph:
 	@echo "cluster    staph"; \
 	pangraph cluster -d data/staph data/staph/assemblies/*.fna.gz
 	@echo "build      staph"; \
-	pangraph build -d data/staph -m 500 -b 0 -e 2500 -w 1000 data/staph/guide.json 1>staph-e2500-w1000.log 2>/dev/null
+	pangraph build -d data/staph -m 500 -b 0 -e 2500 -w 100 data/staph/guide.json
 
 # figures
 
diff --git a/pangraph/build.py b/pangraph/build.py
index 5c3a8ec..e744149 100644
--- a/pangraph/build.py
+++ b/pangraph/build.py
@@ -81,7 +81,7 @@ def main(args):
     mkdir(tmp)
 
     log("aligning")
-    T.align(tmp, args.len, args.mu, args.beta, args.extensive, args.statistics)
+    T.align(tmp, args.len, args.mu, args.beta, args.extensive, args.window, args.extend, args.statistics)
     # TODO: when debugging phase is done, remove tmp directory
 
     graphs = T.collect()
diff --git a/pangraph/graph.py b/pangraph/graph.py
index 83ef839..f4afa97 100644
--- a/pangraph/graph.py
+++ b/pangraph/graph.py
@@ -163,7 +163,7 @@ class Graph(object):
     # ---------------
     # methods
 
-    def union(self, qpath, rpath, out, cutoff=0, alpha=10, beta=2, edge_window=100, edge_extend=2500, extensive=False):
+    def union(self, qpath, rpath, out, cutoff=0, alpha=10, beta=2, extensive=False, edge_window=1000, edge_extend=2500):
         from seqanpy import align_global as align
 
         # ----------------------------------
diff --git a/pangraph/tree.py b/pangraph/tree.py
index 64ac119..eeb52c8 100644
--- a/pangraph/tree.py
+++ b/pangraph/tree.py
@@ -292,7 +292,7 @@ class Tree(object):
         leafs = {n.name: n for n in self.get_leafs()}
         self.seqs = {leafs[name]:seq for name,seq in seqs.items()}
 
-    def align(self, tmpdir, min_blk_len, mu, beta, extensive, log_stats=False, verbose=False):
+    def align(self, tmpdir, min_blk_len, mu, beta, extensive, edge_window, edge_extend, log_stats=False, verbose=False):
         self.root.set_level(0) # NOTE: for debug logging
         stats = {}
         # ---------------------------------------------
@@ -351,7 +351,7 @@ class Tree(object):
                 graph1, fapath1 = node1.graph, node1.fapath
                 graph2, fapath2 = node2.graph, node2.fapath
                 graph    = Graph.fuse(graph1, graph2)
-                graph, _ = graph.union(fapath1, fapath2, f"{tmpdir}/{n.name}", min_blk_len, mu, beta, extensive)
+                graph, _ = graph.union(fapath1, fapath2, f"{tmpdir}/{n.name}", min_blk_len, mu, beta, extensive, edge_window, edge_extend)
             else:
                 graph = node1.graph
 
@@ -361,7 +361,7 @@ class Tree(object):
                 itr = f"{tmpdir}/{n.name}_iter_{i}"
                 with open(f"{itr}.fa", 'w') as fd:
                     graph.write_fasta(fd)
-                graph, contin = graph.union(itr, itr, f"{tmpdir}/{n.name}_iter_{i}", min_blk_len, mu, beta, extensive)
+                graph, contin = graph.union(itr, itr, f"{tmpdir}/{n.name}_iter_{i}", min_blk_len, mu, beta, extensive, edge_window, edge_extend)
                 if not contin:
                     return graph
             return graph