First commit.

RenderTree.py

@@ -0,0 +1,62 @@
+# Copyright (c) 2015 William Lees
+
+# Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
+# documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit
+# persons to whom the Software is furnished to do so, subject to the following conditions:
+
+# The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
+# Software.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
+# WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+# OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+# Various methods to render trees for the website
+
+__author__ = 'William Lees'
+__docformat__ = "restructuredtext en"
+
+from ete2 import Tree, TreeStyle, TextFace, NodeStyle
+
+class RenderTree():
+    def __init__(self):
+        pass
+
+    @staticmethod
+    def render_annotate(newick_path, output_path):
+        """Render the annotated tree, showing internal node names.
+           The output_path should end in .PNG, .PDF or .SVG: this will determine the format.
+
+           To aid in testing, if output_path is None, the tree is shown rather than rendered.
+        """
+        tree = Tree(newick_path, format=1)
+
+        ts = TreeStyle()
+        ts.show_leaf_name = True
+        ts.branch_vertical_margin = 15
+
+        ns = NodeStyle()
+        ns["size"] = 1
+
+        edge = 0
+        for node in tree.traverse():
+            node.name = node.name.replace("'", "")
+            node.name = node.name.replace("+", ",")
+            if not node.is_leaf() and node.name != 'NoName':
+                f = TextFace(node.name)
+                f.margin_top = 5
+                f.margin_bottom = 5
+                f.margin_right = 10
+                f.margin_left = 10
+                edge += 1
+                node.add_face(f, column=0, position="branch-top")
+
+        if output_path is None:
+            tree.show(tree_style=ts)
+        else:
+            tree.render(output_path)
+
+if __name__ == '__main__':
+    RenderTree.render_annotate("C:\\Users\\william\\Dropbox (Personal)\\Research\\TreeAnnotateApp\\temp\\tmpviamgd\\annotated_treefile.new", None)

testfiles/.gitignore

@@ -1,4 +1,6 @@
 summarise_test_aa.txt
 summarise_test_n.txt
 extract_test_out.fasta
-imgt_germlines.fasta
+imgt_germlines.fasta
+C265
+test_Cluster265_germlines_g_j.fasta