diff --git a/src/concatFiles.py b/src/concatFiles.py index 0c19cc11bb48b5fd5910574c6fcd5bab5460c05b..f09bc060cbcba85a16a82d95d88e8c99d9f2f765 100755 --- a/src/concatFiles.py +++ b/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) diff --git a/src/ete.py b/src/ete.py index ae376e7de2788ae706bd285141b0ced917310cd4..f80b9fab5f4f0da970670772fc98d8055b714367 100755 --- a/src/ete.py +++ b/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])) diff --git a/src/nejo_idx.py b/src/nejo_idx.py index ddc57fbe511ff1555174e124faf3851a94d2add6..9532e8ddaf215d00c9035c07f070a650faac9532 100755 --- a/src/nejo_idx.py +++ b/src/nejo_idx.py @@ -1,5 +1,7 @@ #!/usr/bin/env python3 +# author: Stefan Kurtz + import sys, argparse import numpy as np from ete3 import Tree diff --git a/src/phybema.py b/src/phybema.py index cc8c63311bc09b68fe6f87687e0bddc504b725e5..2e941510984944c9102dea40b2cc54303048f30f 100755 --- a/src/phybema.py +++ b/src/phybema.py @@ -2,7 +2,7 @@ ''' Main script for calling phybema -author: Birgitta Päuker +authors: Birgitta Päuker, Stefan Kurtz ''' import sys, os, shutil