Removing stand alones and addind author information

src/concatFiles.py

@@ -25,15 +25,3 @@ def concat_files(infiles, outfilepath):
                      .format(sys.argv[0]))
     exit(1)
 
-def parse_command_line():
-  p = argparse.ArgumentParser()
-  p.add_argument("inputfiles", nargs = '+',
-                 help = "Specify a list of inputfiles to concatenate.\n")
-  p.add_argument("outfilename",
-                 help = "Specify the filename of the concatenated files.\n")
-  args = p.parse_args()
-  return args
-
-if __name__ == "__main__":
-  args = parse_command_line()
-  concat_files(args.inputfiles, args.outfilename)

src/ete.py

@@ -63,37 +63,3 @@ def compute_nrf_matrix(newickfilelist):
       linedict[j] = nrf
     nrf_matrix[i] = linedict
   return nrf_matrix
-
-def parse_command_line():
-  p = argparse.ArgumentParser()
-  p.add_argument('-o', '--out', type=str,
-                 help = "specify outputfile to render tree from inputfile\n"
-                 "It has to be PDF, PNG or SVG")
-  p.add_argument('-c', '--compare', nargs= '+', default = None,
-                 help="whitespace separated files of trees for"
-                 "comparison with inputfile tree. "
-                 "If -c is the last optional argument write --"
-                 "at the end of the list")
-  p.add_argument("inputfile", type=str, help="specify inputfile."
-                 "Inputfile serves as reference tree for comparison")
-  args = p.parse_args()
-
-  if not (args.out or args.compare):
-    sys.stderr.write("Usage {}: Please choose an option for the given "
-                   "tree\n".format(sys.argv[0]))
-    exit(1)
-  return args
-
-if __name__ == "__main__":
-  args = parse_command_line()
-  t = load_tree(args.inputfile)
-
-  if args.out:
-    show_tree(args.inputfile, args.out)
-
-  if args.compare:
-    i = 0
-    for fp in args.compare:
-      t2 = load_tree(fp)
-      rf = rf_dist.robinson_foulds_ete(t,t2)
-      print("{}\t{:.2}".format(fp, rf[2]))

src/nejo_idx.py

 #!/usr/bin/env python3
 
+# author: Stefan Kurtz
+
 import sys, argparse
 import numpy as np
 from ete3 import Tree

src/phybema.py

@@ -2,7 +2,7 @@
 
 '''
 Main script for calling phybema
-author: Birgitta Päuker
+authors: Birgitta Päuker, Stefan Kurtz
 '''
 
 import sys, os, shutil