remove redundant comments

Author: Mai To Uyen

Software/CHANGELOG.md

@@ -1,5 +1,5 @@
 *  Vertion 1.4.0:
-    * Major release. Allow calibration for internal nodes. Requires unique labeling for all nodes and sampling times / calibration points are identified by node labels.
+    * Major release. Allow calibrations for internal nodes and allow missing sampling times for leaves; hard constraints only. Requires unique labeling for all nodes and sampling times / calibration points are identified by node labels.
 *  Version 1.3.1:
     * Added zero-length and verbose options. Remove options for LSD and LF. Remove options for scaling. Remove cvxpy requirement.  
 *  Version 1.3.0:

Software/launch_LogDate.py

@@ -23,14 +23,11 @@
 parser.add_argument("-r","--rootAge",required=False,help="Root age. Can be used with either -f or -t, but not both. Default: None if -t is specified else 0")
 parser.add_argument("-f","--leafAge",required=False,help="Leaf age. To be used with root age to infer relative time. Will be overried by -t if -t is specified. Default: None if -t is specified else 1.")
 parser.add_argument("-o","--output",required=True,help="The output trees with branch lengths in time unit.")
-#parser.add_argument("-d","--tempdir",required=False,help="The output from lsd will be kept in the specified directory")
-#parser.add_argument("-e","--pseudo",action='store_true',help="Can only be used with wLogDate. Control pseudo-count branches. Default: NO")
 parser.add_argument("-v","--verbose",action='store_true',help="Show verbose message. Default: NO")
 parser.add_argument("-p","--rep",required=False,help="The number of random replicates for initialization. Default: use 1 initial point")
 parser.add_argument("-s","--rseed",required=False,help="Random seed to generate starting tree initial points")
 parser.add_argument("-l","--seqLen",required=False,help="The length of the sequences. Default: 1000")
 parser.add_argument("-m","--maxIter",required=False,help="The maximum number of iterations for optimization. Default: 50000")
-#parser.add_argument("-q","--scale",required=False,help="Scaling strategy. Either None, sqrt, or linear. Default: None")
 parser.add_argument("-u","--addpseudo",required=False,help="Add pseudo counting for per-branch weighting.Default: 0.01")
 parser.add_argument("-z","--zero",required=False,help="Set zero-length branches (if any) to this number. LogDate cannot process zero-length branches. Default: 1e-10")
 
@@ -50,7 +47,6 @@
 pseudo = 0.01 if args["addpseudo"] is None else float(args["addpseudo"])
 maxIter = int(args["maxIter"]) if args["maxIter"] else 50000
 randseed = int(args["rseed"]) if args["rseed"] else None
-#scale = args["scale"] if args["scale"] else None
 zero_len = float(args["zero"]) if args["zero"] else 1e-10
 
 brScale = None
@@ -62,56 +58,8 @@
     if node is not tree.seed_node and node.edge_length == 0:
         node.edge_length = zero_len
 
-'''
-if objective == "LF":
-    f_obj = f_LF
-elif objective == "LSD":
-    f_obj = f_lsd
-elif objective == "PL":
-    f_obj = f_PL    
-elif objective == "LogDate":    
-    if scale == 'sqrt':
-        f_obj = f_logDate_sqrt_scale
-    elif scale == 'linear':
-        f_obj = f_logDate_linear_scale
-    else:    
-        f_obj = f_logDate
-elif objective == "wLogDate":
-    if scale == 'sqrt':
-        f_obj = f_wlogDate_sqrt_scale 
-    elif scale=='linear':
-        f_obj = f_wlogDate_linear_scale
-    else:
-        f_obj = f_logDate_sqrt_b 
-    
-    #brScale = "sqrt"            
-
-
-if args["pseudo"]:
-    smpl_time = {}
-    with open(sampling_time,'r') as fin:
-        fin.readline()
-        for line in fin:
-            taxon,time = line.split()
-            smpl_time[taxon] = float(time)
-    x,f = log_from_random_init(tree,smpl_time,root_age=rootAge,leaf_age=leafAge,brScale=brScale,nrep=nrep,min_nleaf=3,maxIter=maxIter,seed=randseed)
-    write_time_tree(tree,outfile=args["output"])
-    print("Best log-scored solution: ")
-    print("Log score: " + str(f))
-    print("Clock rate: " + str(x[1]))
-    print("Root age: " + str(x[0]/x[1]))
-else:
-    if objective == "LF":
-        mu,f,x,s_tree,t_tree = run_LF_cvxpy(tree,sampling_time=sampling_time,root_age=rootAge,leaf_age=leafAge)
-    elif objective == "PL":
-        mu,f,x,s_tree,t_tree = logDate_with_penalize_llh(tree,sampling_time=sampling_time,root_age=rootAge,leaf_age=leafAge,maxIter=maxIter)
-    else:
-        mu,f,x,s_tree,t_tree = logDate_with_random_init(tree,f_obj,sampling_time=sampling_time,root_age=rootAge,leaf_age=leafAge,nrep=nrep,min_nleaf=10,maxIter=maxIter,seed=randseed,scale=scale,pseudo=pseudo,seqLen=seqLen)'''
-
 mu,f,x,s_tree,t_tree = logDate_with_random_init(tree,f_obj,sampling_time=sampling_time,root_age=rootAge,leaf_age=leafAge,nrep=nrep,min_nleaf=10,maxIter=maxIter,seed=randseed,pseudo=pseudo,seqLen=seqLen,verbose=verbose)
 tree_as_newick(t_tree,outfile=args["output"],append=False)
 
-#t_tree_swift = treeswift.read_tree_dendropy(t_tree)
-#t_tree_swift.write_tree_newick(args["output"])
 print("Clock rate: " + str(mu))
 print("Log score: " + str(f))