updated

src/join_paftol_tax.py

@@ -0,0 +1,55 @@
+import sys
+import node
+import tree_reader
+import tree_utils
+
+def process_tax(t):
+    return
+
+def get_mrca_wnms(n,t):
+    if len(n) == 1:
+        for i in t.leaves():
+            if i.label == n[0]:
+                return i
+    else:
+        return tree_utils.get_mrca_wnms(n,t)
+
+if __name__ == "__main__":
+    if len(sys.argv) != 3:
+        print("python",sys.argv[0],"paf tax")
+        sys.exit(0)
+
+    paf = tree_reader.read_tree_file_iter(sys.argv[1]).__next__()
+    tax = tree_reader.read_tree_file_iter(sys.argv[2]).__next__()
+
+    for i in paf.leaves():
+        i.data["original_name"] = i.label
+        i.label = i.label.split("_")[-1]
+    for i in tax.leaves():
+        i.data["original_name"] = i.label
+        i.label = i.label.split("_")[0]
+    count= 0
+    for i in paf.iternodes(order="postorder"):
+        if len(i.children) < 2:
+            continue
+        l = i.lvsnms()
+        print(l,file=sys.stderr)
+        p = get_mrca_wnms(l,tax)
+        chds = []
+        for j in i.children:
+            k = get_mrca_wnms(j.lvsnms(),tax)
+            if k == None:
+                continue
+            chds.append(k)
+        if len(chds) == 1:
+            continue
+        n = node.Node()
+        for j in chds:
+            pp = j.parent # need to add here if it is non-monophyletic so that things get sunk as a result
+            pp.remove_child(j)
+            n.add_child(j)
+        p.add_child(n)
+        count += 1
+        if count == 21:
+            break
+    print(tax.get_newick_repr(False))

src/process_paftol.py

@@ -0,0 +1,48 @@
+import sys
+
+import node
+import tree_reader
+
+def get_name(nm):
+    nm = nm.replace("'","").replace(" ","_")
+    nm = "_".join(nm.split("_")[:-1])
+    return nm
+
+if __name__ == "__main__":
+    if len(sys.argv) != 2:
+        print("python",sys.argv[0],"tre")
+        sys.exit(0)
+
+    t = tree_reader.read_tree_file_iter(sys.argv[1]).__next__()
+    for i in t.leaves():
+        i.label = get_name(i.label)
+
+    # check for monophyly and sink
+    going = True
+    while going:
+        going = False
+        for i in t.iternodes("postorder"):
+            lvs = i.leaves()
+            x = set(i.lvsnms())
+            if len(x) == 1 and len(lvs) > 1:
+                going = True
+                p = i.parent
+                i.parent.children.remove(i)
+                i.parent = None
+                nd = node.Node()
+                nd.istip = True
+                nd.label = list(x)[0]
+                p.add_child(nd)
+                break
+    going = True
+    while going:
+        going = False
+        for i in t.iternodes():
+            if len(i.children) == 1:
+                p = i.parent
+                c = i.children[0]
+                p.children.remove(i)
+                i.parent = None
+                p.add_child(c)
+                going = True
+    print(t.get_newick_repr(False)+";")