add nexus newick script

scripts/nexus2newick.py

@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+"""
+@author: Katherine Eaton
+
+Convert Nexus tree to Newick Format.
+
+./nexus2newick.py --nexus tree.nexus --newick tree.nwk
+"""
+
+# This program should only be called from the command-line
+if __name__ != "__main__": quit()
+
+#-----------------------------------------------------------------------#
+#                         Modules and Packages                          #
+#-----------------------------------------------------------------------#
+import argparse                         # Command-line argument parsing
+import dendropy                         # Read and write trees
+
+#-----------------------------------------------------------------------#
+#                            Argument Parsing                           #
+#-----------------------------------------------------------------------#
+
+parser = argparse.ArgumentParser(description='Convert Nexus tree to Newick Format.',
+                                 add_help=True)
+
+# Argument groups for the program
+
+parser.add_argument('--nexus',
+                    help = 'Path to the input nexus tree.',
+                    action = 'store',
+                    dest = 'nexusPath',
+                    required = True)
+
+parser.add_argument('--newick',
+                    help = 'Path to the output newick tree.',
+                    action = 'store',
+                    dest = 'newickPath',
+                    required = True)
+
+# Retrieve user parameters
+args = vars(parser.parse_args())
+
+nexus_path = args['nexusPath']
+newick_path = args['newickPath']
+
+#------------------------------------------------------------------------------#
+#                                Error Catching                                #
+#------------------------------------------------------------------------------#
+post_trees = dendropy.TreeList()
+
+# Check if  NEXUS file exists
+if not os.path.exists(nexus_path):
+    print('An error occurred while trying to open', nexus_path)
+    sys.exit(1)
+
+post_trees.read(
+  file=open(nexus_path, "r"),
+  schema="nexus")
+
+post_trees.write(
+  path=newick_path,
+  schema="newick")