# Copyright 2007 by Tiago Antao . # Revisions copyright 2014 by Melissa Gymrek . # All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """This module allows you to control Simcoal2 and FastSimcoal (DEPRECATED).""" import os import sys from Bio.Application import AbstractCommandline, _Option, _Switch class SimCoalController(object): def __init__(self, simcoal_dir): """Initializes the controller. (DEPRECATED) simcoal_dir is the directory where simcoal is. The initializer checks for existence and executability of binaries. """ self.simcoal_dir = simcoal_dir self.os_name = os.name # remove this? dir_contents = os.listdir(self.simcoal_dir) # We expect the tool to be installed as simcoal2(.exe) # without any trailing version number. self.bin_name = "simcoal2" if self.bin_name not in dir_contents: # Try case insensitive, dir_contents = [x.lower() for x in dir_contents] if self.bin_name not in dir_contents: # Try with .exe self.bin_name += '.exe' if self.bin_name not in dir_contents: raise IOError("SimCoal not available") if not os.access(os.path.join(self.simcoal_dir, self.bin_name), os.X_OK): raise IOError("SimCoal not executable") def run_simcoal(self, par_file, num_sims, ploydi='1', par_dir='.'): """Executes SimCoal. """ if par_dir is None: par_dir = os.sep.join([".", 'SimCoal', 'runs']) curr_dir = os.getcwd() # TODO - Make sure we change drive on Windows as well? os.chdir(par_dir) exe = os.path.join(self.simcoal_dir, self.bin_name) if " " in exe: exe = '"' + exe + '"' cmd = exe + ' ' + par_file + ' ' + str(num_sims) + ' ' + ploydi # TODO - Better way to spot if on Jython on Windows? if sys.platform == "win32" or self.bin_name.endswith(".exe"): # There is no /dev/nul on Windows cmd += ' > nul 2>nul' else: cmd += ' >/dev/null 2>&1' os.system(cmd) os.chdir(curr_dir) class _FastSimCoalCommandLine(AbstractCommandline): """ Command Line Wrapper for Fastsimcoal """ def __init__(self, fastsimcoal_dir=None, cmd='fastsimcoal', **kwargs): self.parameters = [ _Option(["-i", "--ifile", "parfile"], "Name of the parameter file", filename=True, equate=False, is_required=False, checker_function=lambda x: isinstance(x, str)), _Option(["-n", "--numsims", "numsims"], "Number of simulations to perform", filename=False, equate=False, is_required=True, checker_function=lambda x: isinstance(x, int)), _Option(["-t", "--tfile", "tfile"], "Name of template parameter file", filename=True, equate=False, is_required=False, checker_function=lambda x: isinstance(x, str)), _Option(["-f", "--dfile", "dfile"], "Name of parameter definition file", filename=True, equate=False, is_required=False, checker_function=lambda x: isinstance(x, str)), _Option(["-F", "--dFile", "dFile"], """Same as -f but only uses simple parameters defined in the template file. Complex params are recomputed""", filename=True, equate=False, is_required=False, checker_function=lambda x: isinstance(x, str)), _Option(["-e", "--efile", "efile"], """Parameter prior definition file. Parameters drawn from specified distributions are substituted into template file.""", filename=True, equate=False, is_required=False, checker_function=lambda x: isinstance(x, str)), _Option(["-E", "--numest", "numest"], """Number of estimations from parameter priors. Listed parameter values are substituted in template file.""", filename=False, equate=False, is_required=False, checker_function=lambda x: isinstance(x, int)), _Switch(["-g", "--genotypic", "genotypic"], "Generates Arlequin projects with genotypic data"), _Switch(["-p", "--phased", "phased"], "Specifies that phase is known in Arlequin output"), _Option(["-s", "--dnatosnp", "dnatosnp"], """"Output DNA as SNP data (0: ancestral, 1: derived and specify maximum no. SNPs to output.""", filename=False, equate=False, is_required=False, checker_function=lambda x: isinstance(x, int)), _Switch(["-S", "--allsites", "allsites"], """Output the whole DNA sequence, including monomorphic sites"""), _Switch(["-I", "--inf", "inf"], """Generates DNA mutations according to an infinite sites (IS) mutation model."""), _Switch(["-d", "--dsfs", "dsfs"], "Computes derived site frequency spectrum"), _Switch(["-m", "--msfs", "msfs"], "Computes minor site frequency spectrum"), _Option(["-o", "--oname", "oname"], "Generic name for observed SFS files", filename=False, equate=False, is_required=False, checker_function=lambda x: isinstance(x, str)), _Switch(["-H", "--header", "header"], "Generates header in site frequency spectrum files."), _Switch(["-q", "--quiet", "quiet"], "Minimal messages output to console"), _Switch(["-T", "--tree", "tree"], "Output coalescent tree in nexus format."), _Option(["-k", "--keep", "keep"], """Number of simulated polymorphic sites kept in memory. If the simulated no. is larger, then temporary files are created.""", filename=False, equate=False, is_required=False, checker_function=lambda x: isinstance(x, int)), _Option(["--seed", "seed"], "Seed for the random number generator (positive int <=1E6)", filename=False, equate=False, is_required=False, checker_function=lambda x: isinstance(x, int)), _Switch(["-x", "--noarloutput", "noarloutput"], "Does not generate Arlequin output"), _Switch(["-D", "--dadioutput", "dadioutput"], "Output SFS in dadi format"), _Option(["-M", "--maxlhood", "maxlhood"], """Perform parameter estimation by max lhood from SFS, and define stop criterion as min., rel., diff. in parameter values between iterations""", filename=False, equate=False, is_required=False, checker_function=lambda x: isinstance(x, float)), _Option(["-N", "--maxnumsims", "maxnumsims"], """Maximum number of simulations to perform during likelihood maximization.""", filename=False, equate=False, is_required=False, checker_function=lambda x: isinstance(x, int)), _Option(["-l", "--minnumloops", "minnumloops"], """Minimum number of iteration loops to perform during likelihood maximization.""", filename=False, equate=False, is_required=False, checker_function=lambda x: isinstance(x, int)), _Option(["-L", "--maxnumloops", "maxnumloops"], """Maximum number of iterations to perform during likelihood maximization""", filename=False, equate=False, is_required=False, checker_function=lambda x: isinstance(x, int)), _Option(["-C", "--minSFSCount", "minSFSCount"], """Minimum observed SFS entry count taken into account in likelihood computation""", filename=False, equate=False, is_required=False, checker_function=lambda x: isinstance(x, int)), _Switch(["-0", "--removeZeroSFS", "removeZeroSFS"], """Do not take into account monomorphic sites for SFS likelihood computation."""), _Option(["-a", "--ascDeme", "ascDeme"], """This is the deme id where ascertainment is performed when simulating SNPs.""", filename=False, equate=False, is_required=False, checker_function=lambda x: isinstance(x, int)), _Option(["-A", "--ascSize", "ascSize"], """Number of ascertained chromosomes used to define SNPs in a given deme.""", filename=False, equate=False, is_required=False, checker_function=lambda x: isinstance(x, int)), _Switch(["-u", "--multiSFS", "multiSFS"], "Generate or use multidimensional SFS")] AbstractCommandline.__init__(self, cmd, **kwargs) class FastSimCoalController(object): def __init__(self, fastsimcoal_dir=None, bin_name="fsc252"): """Initializes the controller. fastsimcoal_dir is the directory where fastsimcoal is. By default the binary should be called fsc252. bin_name specifies a different name for the binary. The initializer checks for existence and executability of binaries and sets up the command line controller. Fastsimcoal2 is available here: http://cmpg.unibe.ch/software/fastsimcoal2/. This wrapper was written and tested for fastsimcoal version 2.51. """ self.bin_name = bin_name self.fastsimcoal_dir = fastsimcoal_dir if fastsimcoal_dir is None: for path in os.environ["PATH"].split(os.pathsep): if os.path.isfile(os.path.join(path, self.bin_name)): self.fastsimcoal_dir = path if self.fastsimcoal_dir is None: raise IOError("Fastsimcoal not available") else: dir_contents = os.listdir(fastsimcoal_dir) if self.bin_name not in dir_contents: raise IOError("Fastsimcoal not available") if not os.access(os.path.join(self.fastsimcoal_dir, self.bin_name), os.X_OK): raise IOError("Fastsimcoal not executable") def run_fastsimcoal(self, par_file, num_sims, par_dir='.', opts=None): """Executes Fastsimcoal. par_file is the input parameter file (--ifile) for fastsimcoal. num_sims is the number of simulations to perform. par_dir is the directory where par_file is and where output will be written. opts is a dictionary of additional options to fastsimcoal. """ if opts is None: opts = {} if par_dir is None: par_dir = os.sep.join([".", "Fastsimcoal", "runs"]) if not os.path.exists(par_dir): os.mkdir(par_dir) curr_dir = os.getcwd() os.chdir(par_dir) if par_file is None: # Must use .tpl for -t instead if no par_file controller = _FastSimCoalCommandLine(cmd=os.path.join(self.fastsimcoal_dir, self.bin_name), numsims=num_sims, **opts) else: controller = _FastSimCoalCommandLine(cmd=os.path.join(self.fastsimcoal_dir, self.bin_name), parfile=par_file, numsims=num_sims, **opts) controller() os.chdir(curr_dir)