Commit d232141756b05ac46b0d25a2ec0ae4224d216442

Authored by Jean-Michel Garant
1 parent 3e548338
Exists in master

default merge.py for input file only

Showing 4 changed files with 15 additions and 9 deletions   Show diff stats
g4base.py
1 1 #!/usr/bin/env python2.7
2 2  
3 3 # Identification of potential RNA G-quadruplexes by G4RNA screener.
4   -# Copyright (C) 2018 Jean-Michel Garant
  4 +# Copyright (C) 2019 Jean-Michel Garant
5 5 #
6 6 # This program is free software: you can redistribute it and/or modify
7 7 # it under the terms of the GNU General Public License as published by
... ...
merge.py
1 1 #!/usr/bin/env python2.7
2 2  
3 3 # Identification of potential RNA G-quadruplexes by G4RNA screener.
4   -# Copyright (C) 2018 Jean-Michel Garant
  4 +# Copyright (C) 2019 Jean-Michel Garant
5 5 #
6 6 # This program is free software: you can redistribute it and/or modify
7 7 # it under the terms of the GNU General Public License as published by
... ... @@ -183,9 +183,9 @@ def arguments():
183 183 # declare argument parser
184 184 parser = argparse.ArgumentParser(formatter_class=utils.Formatter,
185 185 prog=os.path.basename(__file__),
186   - description="[WORK IN PROGRESS] [DO NOT DISTRIBUTE] Merge positive windows of screen.py output and "\
  186 + description="Merge positive windows of screen.py output and "\
187 187 "discard windows below the threshold(s)",
188   - epilog="G4RNA screener Copyright (C) 2018 Jean-Michel Garant "\
  188 + epilog="G4RNA screener Copyright (C) 2019 Jean-Michel Garant "\
189 189 "This program comes with ABSOLUTELY NO WARRANTY. This is free "\
190 190 "software, and you are welcome to redistribute it under certain "\
191 191 "conditions <http://www.gnu.org/licenses/>.")
... ... @@ -220,8 +220,9 @@ def arguments():
220 220 choices=[float_range(0,1)],
221 221 default=False,
222 222 help="Use G4NN score threshold to determine positive windows "\
223   - "(default: 0.5)",
224   - metavar="FLOAT")
  223 + "* Used when no threshold are defined in arguments "\
  224 + "* (default: 0.5)",
  225 + metavar="*FLOAT*")
225 226 # windows length
226 227 parser.add_argument("-w", "--window",
227 228 type=int,
... ... @@ -255,6 +256,11 @@ def arguments():
255 256 parser.print_help()
256 257 parser.exit()
257 258 args = parser.parse_args()
  259 + # the next if statement checks if there is a single argument (input file)
  260 + # in this case the default filter/threshold is G4NN
  261 + if len(sys.argv[1:])==1:
  262 + args.G4NN = 0.5
  263 + # default thresholds values
258 264 if args.cGcC == None:
259 265 args.cGcC = 4.5
260 266 if args.G4H == None:
... ...
screen.py
1 1 #!/usr/bin/env python2.7
2 2  
3 3 # Identification of potential RNA G-quadruplexes by G4RNA screener.
4   -# Copyright (C) 2018 Jean-Michel Garant
  4 +# Copyright (C) 2019 Jean-Michel Garant
5 5 #
6 6 # This program is free software: you can redistribute it and/or modify
7 7 # it under the terms of the GNU General Public License as published by
... ... @@ -225,7 +225,7 @@ def arguments():
225 225 parser = argparse.ArgumentParser(formatter_class=utils.Formatter,
226 226 prog=os.path.basename(__file__),
227 227 description="Identification of potential RNA G-quadruplexes",
228   - epilog="G4RNA screener Copyright (C) 2018 Jean-Michel Garant "\
  228 + epilog="G4RNA screener Copyright (C) 2019 Jean-Michel Garant "\
229 229 "This program comes with ABSOLUTELY NO WARRANTY. This is free "\
230 230 "software, and you are welcome to redistribute it under certain "\
231 231 "conditions <http://www.gnu.org/licenses/>.")
... ...
utils.py
1 1 #!/usr/bin/env python2.7
2 2  
3 3 # Identification of potential RNA G-quadruplexes by G4RNA screener.
4   -# Copyright (C) 2018 Jean-Michel Garant
  4 +# Copyright (C) 2019 Jean-Michel Garant
5 5 #
6 6 # This program is free software: you can redistribute it and/or modify
7 7 # it under the terms of the GNU General Public License as published by
... ...