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ms_ps.py
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ms_ps.py
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# -*- mode: python; coding: utf-8; -*-
# ms_ps.py - simulate coalescent with partial-selfing with Hudson's ms.
# Copyright (C) 2012 Seiji Kumagai
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice (including the next
# paragraph) shall be included in all copies or substantial portions of the
# Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
import os
import sys
from subprocess import call
from scipy.stats import binom
MSPATH="./msdir/ms"
def is_exe(fpath):
return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
def which(program):
fpath, fname = os.path.split(program)
if fpath:
if is_exe(program):
return program
else:
for path in os.environ["PATH"].split(os.pathsep):
exe_file = os.path.join(path, program)
if is_exe(exe_file):
return exe_file
return None
def run_ms(args):
program = 'ms'
if which('ms') is None:
if is_exe(MSPATH) is None:
sys.exit(1)
else:
program = MSPATH
command = [program]
command.extend(args)
if int(args[0]) > 1:
call(command)
def adjust_args(args):
idx = args.index('-S')
s = float(args[idx + 1])
p = s / (2.0 - s)
del args[idx:idx+2]
# Adjust demographic parameters (Nordborg & Donnelly (1997) and
# Nordborg (2000))
# mutation rate: \theta_eff = \theta * (2 - s) / s
if '-t' in args:
idx = args.index('-t')
args[idx+1] = str(float(args[idx+1]) * (2.0 - s) / 2.0)
# recombination: \rho_eff = \rho * (1 - s)
if '-r' in args:
idx = args.index('-r')
args[idx+1] = str(float(args[idx+1]) * (1.0 - s))
if '-I' in args:
idx = args.index('-I')
npops = int(args[idx + 1])
start = idx + 2
stop = start + npops
for n in range(start, stop):
# binom(int(
args[n] = str(int(args[n]) -
binom.rvs(int(args[n+npops]), p))
args[0] = str(sum([int(i) for i in args[start:stop]]))
start += npops
stop += npops
del args[start:stop]
else:
args[0] = str(int(args[0]) -
binom.rvs(int(args[2]), p))
del args[2]
return args
if __name__ == '__main__':
args = sys.argv[1:]
if '-S' in args:
# 'Partial selfing is present in a model'
run_ms(adjust_args(args))
else:
# No partial-selfing. Use ms as-is.
run_ms(args)