#!/usr/bin/python

# Creates a throw-away profile based on standard command-line options.

from sys import argv

sim_only = False
trials = 1
generations = 1000
pop_size = 500
selection = 'N'
drift = 'N'
selection_coeff = 0.5
drift_start = 500
drift_duration = 498
drift_size = 250
mutation_rate = 0.000034
recombination_rate = 0.000024
transition_ratio = 1.3

for i in range (len (argv)):
  if i == 0:
    pass
  elif argv[i] == '-so':
    sim_only = True
  elif argv[i].startswith ('-t'):
    trials = int (argv[i][2:])
  elif argv[i].startswith ('-g'):
    generations = int (argv[i][2:])
  elif argv[i].startswith ('-ps'):
    pop_size = int (argv[i][3:])
  elif argv[i].startswith ('-se'):
    selection = argv[i][3]
  elif argv[i].startswith ('-dr'):
    drift = argv[i][3]
  elif argv[i].startswith ('-sc'):
    selection_coeff = float (argv[i][3:])
  elif argv[i].startswith ('-dst'):
    drift_start = int (argv[i][4:])
  elif argv[i].startswith ('-dd'):
    drift_duration = int (argv[i][3:])
  elif argv[i].startswith ('-dsi'):
    drift_size = int (argv[i][4:])
  elif argv[i].startswith ('-mm'):
    mutation_rate = float (argv[i][3:])
  elif argv[i].startswith ('-mr'):
    recombination_rate = float (argv[i][3:])
  elif argv[i].startswith ('-mt'):
    transition_ratio = float (argv[i][3:])
  else:
    print "Unknown argument: " + argv[i]

if sim_only:
  print "simulation-only make-profile"

if selection == 'p':
  print "selection-model: purifying"
elif selection == 'd':
  print "selection-model: diversifying"

if drift == 's':
  print "drift-model: even-subdivision"
elif drift == 'b':
  print "drift-model: sharp-bottleneck"

print "trials: " + str (trials)
print "generations: " + str (generations)
print "population-size: " + str (pop_size)
print "sample-size: " + str (pop_size)
print "purifying-selection-coefficient: " + str (selection_coeff)
print "diversifying-selection-coefficient: " + str (selection_coeff)
print "sharp-bottleneck-start: " + str (drift_start)
print "sharp-bottleneck-duration: " + str (drift_duration)
print "sharp-bottleneck-size: " + str (drift_size)
print "even-subdivision-start: " + str (drift_start)
print "even-subdivision-duration: " + str (drift_duration)
print "even-subdivision-size: " + str (drift_size)
print "mutations-per-nucleotide: " + str (mutation_rate)
print "recombination-rate: " + str (recombination_rate)
print "transitions-per-transversion: " + str (transition_ratio)