fixing run_hyde.py script; adding ignore_amb_sites test

Author: pblischak

Makefile

@@ -5,6 +5,8 @@ all : test test_threads
 test :
 	@printf "**** Testing run_hyde.py (full analysis). ****\n"
 	run_hyde.py -i examples/snake-data.txt -m examples/snake-map.txt -n 52 -t 7 -s 8466 -o out
+	@printf "**** Testing run_hyde.py (ignoring missing/ambiguous sites). ****\n"
+	run_hyde.py -i examples/snake-data.txt -m examples/snake-map.txt -n 52 -t 7 -s 8466 -o out --ignore_amb_sites
 	@printf "\n**** Testing run_hyde.py (using triples). ****\n"
 	run_hyde.py -i test/data.txt -m test/map.txt -o out -tr test/triples.txt -n 16 -t 4 -s 50000
 	@printf "\n**** Testing run_hyde.py (phylip format). ****\n"

phyde/__init__.py

@@ -1,5 +1,5 @@
 
-__version__ = "0.4.2a"
+__version__ = "0.4.3a"
 __author__  = "Paul Blischak and Laura Kubatko"
 
 from phyde.core.bootstrap import Bootstrap

phyde/core/data.pyx

@@ -80,6 +80,7 @@ cdef class HydeData(object):
     :param int ntaxa: the number of populations/taxa.
     :param int nsites: the number of sites.
     :param bool quiet: suppress printing output.
+    :param bool ignore_amb_sites: ignore missing/ambiguous sites.
 
     Example:
 

scripts/run_hyde.py

@@ -118,21 +118,24 @@ def write_out(out, triple, outfile):
                             metavar='\b', help="prefix appended to output files [default=hyde]")
     additional.add_argument('-q', '--quiet', action="store_true",
                             help="supress printing to stdout")
+    additional.add_argument('--ignore_amb_sites', action="store_true",
+                            help="supress printing to stdout")
 
-    args     = parser.parse_args()
-    infile   = args.infile
-    mapfile  = args.map
-    outgroup = args.outgroup
-    nind     = args.num_ind
-    ntaxa    = args.num_taxa
-    nsites   = args.num_sites
-    pvalue   = args.pvalue
-    prefix   = args.prefix
-    quiet    = args.quiet
+    args             = parser.parse_args()
+    infile           = args.infile
+    mapfile          = args.map
+    outgroup         = args.outgroup
+    nind             = args.num_ind
+    ntaxa            = args.num_taxa
+    nsites           = args.num_sites
+    pvalue           = args.pvalue
+    prefix           = args.prefix
+    quiet            = args.quiet
+    ignore_amb_sites = args.ignore_amb_sites
 
     if not quiet: print("\nRunning run_hyde.py")
     # Read in data as HydeData object
-    data = hd.HydeData(infile, mapfile, outgroup, nind, ntaxa, nsites, quiet)
+    data = hd.HydeData(infile, mapfile, outgroup, nind, ntaxa, nsites, quiet, ignore_amb_sites)
 
     # Get triples
     if args.triples != "none":