rename mugration to traits

nextstrain · May 4, 2018 · 28af218 · 28af218
1 parent 778694e
commit 28af218
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/augur/mugration.py → augur/traits.py b/augur/mugration.py → augur/traits.py
diff --git a/bin/augur b/bin/augur
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 import sys
-from augur import align, tree, mugration
+from augur import align, tree, traits
 
 if __name__=="__main__":
     import argparse
@@ -26,13 +26,13 @@ if __name__=="__main__":
     tree_parser.add_argument('--alignment', required=True, help="alignment to build tree from")
     tree_parser.add_argument('--method', default='iqtree', choices=["fasttree", "raxml", "iqtree"], help="tree builder to use")
     tree_parser.add_argument('--output', help='file name to write tree to')
-    tree_parser.add_argument('--iqmodel', help='substitution model to use for iq-tree')
+    tree_parser.add_argument('--iqmodel', default="HKY+F", help='substitution model to use for iq-tree')
     tree_parser.add_argument('--nthreads', type=int, default=2,
                              help="number of threads used by mafft")
     tree_parser.set_defaults(func=tree.run)
 
 
-    ## MUGRATION.PY
+    ## TRAITS.PY
     traits_parser = subparsers.add_parser('traits', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     traits_parser.add_argument('--tree', required=True, help="tree to perform trait reconstruction on")
     traits_parser.add_argument('--metadata', required=True, help="tsv/csv table with meta data")
@@ -41,7 +41,7 @@ if __name__=="__main__":
     traits_parser.add_argument('--confidence',action="store_true",
                         help='record the distribution of subleading mugration states')
     traits_parser.add_argument('--output', default='traits.json', help='')
-    traits_parser.set_defaults(func=mugration.run)
+    traits_parser.set_defaults(func=traits.run)
 
     args = parser.parse_args()
     return_code = args.func(args)