def plots_only(arg):
"""
Handles arrugments and wraps things up for drawing the plots without
running any wrapped programs.
"""
# Relative to abs path
prefix_abs_path = os.path.abspath(arg.prefix)
# Get all files matching the provided prefix
prefix_dir, prefix_name = os.path.split(prefix_abs_path)
if prefix_dir == "":
prefix_dir = "."
k_vals = arg.bestk
if arg.program == "faststructure":
infiles = [
os.path.join(prefix_abs_path, "fS_run_K." + x + ".meanQ")
for x in k_vals
]
elif arg.program == "structure":
infiles = [
os.path.join(prefix_abs_path, "str_K" + x + "_rep1_f")
for x in k_vals
]
else:
infiles = [
os.path.join(os.path.join(prefix_abs_path, "mav_K" + x),
"outputQmatrix_ind_K" + x + ".csv") for x in k_vals
]
for filename in infiles:
sanity.file_checker(
filename, "There was a problem with the deduced "
"filename '{}'. Please check "
"it.".format(filename))
if not infiles:
logging.error("No input files that match the provided prefix. "
"Aborting.")
raise SystemExit
if not os.path.exists(arg.outpath):
os.makedirs(arg.outpath)
bestk = [int(x) for x in arg.bestk]
sp.main(infiles,
arg.program,
arg.outpath,
bestk,
popfile=arg.popfile,
indfile=arg.indfile,
filter_k=bestk,
bw=arg.blacknwhite,
use_ind=arg.use_ind)
def plots_only(arg):
"""
Handles arrugments and wraps things up for drawing the plots without Running
any wrapped programs.
"""
# Get all files matching the provided prefix
prefix_dir, prefix_name = os.path.split(arg.prefix)
if prefix_dir == "":
prefix_dir = "."
if arg.program == "faststructure":
infiles = [
os.path.join(prefix_dir, x) for x in os.listdir(prefix_dir)
if x.startswith(prefix_name) and x.endswith(".meanQ")
]
elif arg.program == "structure":
infiles = [
os.path.join(prefix_dir, x) for x in os.listdir(prefix_dir)
if x.startswith(prefix_name) and "rep1_" in x
]
else:
infiles = [
os.path.join(prefix_dir, x) for x in os.listdir(prefix_dir)
if x.startswith(prefix_name) and x.endswith(".csv")
]
for filename in infiles:
sanity.file_checker(
filename, "There was a problem with the deduced "
"filename '{}'. Please check "
"it.".format(filename))
if not infiles:
logging.error("No input files that match the provided prefix. "
"Aborting.")
raise SystemExit
if not os.path.exists(arg.outpath):
os.makedirs(arg.outpath)
bestk = [int(x) for x in arg.bestk]
sp.main(infiles,
arg.program,
arg.outpath,
bestk,
popfile=arg.popfile,
indfile=arg.indfile,
filter_k=bestk,
bw=arg.blacknwhite,
use_ind=arg.use_ind)
def spooky_scary_skeletons(arg):
"""
Generates skeleton parameter files for STRUCTURE.
"""
try:
import structure_threader.skeletons.stparams as parameters
except ImportError:
import skeletons.stparams as parameters
sanity.file_checker(arg.outpath, is_file=False)
main_file = os.path.join(arg.outpath, "mainparams")
with open(main_file, 'w') as fhandle:
fhandle.write(parameters.MAINPARAMS)
extra_file = os.path.join(arg.outpath, "extraparams")
with open(extra_file, 'w') as fhandle:
fhandle.write(parameters.EXTRAPARAMS)
def argument_sanity(arguments, parser):
"""
Performs some sanity checks on the user provided arguments.
"""
if arguments.main_op == "run":
# External program
sanity.file_checker(
arguments.external_prog, "Could not find your external program in "
"the specified path "
"'{}'.".format(arguments.external_prog))
# Input file
sanity.file_checker(
arguments.infile, "The specified infile '{}' does not "
"exist.".format(arguments.infile))
# Output dir
sanity.file_checker(
arguments.outpath, "Output argument '{}' is pointing to an "
"existing file. This argument requires a "
"directory.".format(arguments.outpath), False)
# Handle argparse limitations with "--" options.
if arguments.extra_options != "":
if "-st" not in sys.argv:
arguments.extra_options = \
"--{0}".format(arguments.extra_options)
arguments.extra_options = \
" --".join(arguments.extra_options.split())
# fastStructure is really only usefull with either a pop or indfile...
if "-fs" in sys.argv and\
arguments.popfile is None and\
arguments.indfile is None:
parser.error("-fs requires either --pop or --ind.")
# Make sure we provide paths for mainparams, extraparams and
# parameters.txt depending on the wrapped program.
if arguments.params is not None:
arguments.params = os.path.abspath(arguments.params)
if "-mv" in sys.argv and arguments.params is None:
parser.error("-mv requires --params.")
elif "-mv" in sys.argv:
sanity.file_checker(os.path.abspath(arguments.params))
elif "-st" in sys.argv and arguments.params is None:
arguments.params = os.path.join(os.path.dirname(arguments.infile),
"mainparams")
# Number of replicates
arguments.replicates = range(1, arguments.replicates + 1)
arguments.threads = sanity.cpu_checker(arguments.threads)
elif arguments.main_op == "plot":
if arguments.program == "faststructure" and arguments.popfile is None\
and arguments.indfile is None:
parser.error("fastStructure plots require either --pop or --ind.")
elif arguments.main_op == "run" or arguments.main_op == "plot":
# Check the existance of several files:
# Popfile
if arguments.popfile is not None:
sanity.file_checker(
arguments.popfile, "The specified popfile '{}' does not "
"exist.".format(arguments.popfile))
# Indfile
if arguments.indfile is not None:
sanity.file_checker(
arguments.indfile, "The specified indfile '{}' does not "
"exist.".format(arguments.indfile))
return arguments
def main():
"""
Main function, where variables are set and other functions get called
from.
"""
# Make sure we provide an help message instead of an error
if len(sys.argv) == 1:
sys.argv += ["-h"]
arg = argument_parser(sys.argv[1:])
# Check the existance of several files:
# Popfile
if arg.popfile is not None:
sanity.file_checker(
arg.popfile, "The specified popfile '{}' does not "
"exist.".format(arg.popfile))
# Indfile
if arg.indfile is not None:
sanity.file_checker(
arg.indfile, "The specified indfile '{}' does not "
"exist.".format(arg.indfile))
# Perform usual structure_threader run
if arg.main_op == "run":
# Switch relative to absolute paths
arg.infile = os.path.abspath(arg.infile)
arg.outpath = os.path.abspath(arg.outpath)
# Figure out which program we are wrapping
if "-fs" in sys.argv:
wrapped_prog = "faststructure"
elif "-mv" in sys.argv:
wrapped_prog = "maverick"
elif "-st" in sys.argv:
wrapped_prog = "structure"
# External program
sanity.file_checker(
arg.external_prog, "Could not find your external program in "
"the specified path "
"'{}'.".format(arg.external_prog))
# Input file
sanity.file_checker(
arg.infile, "The specified infile '{}' does "
"not exist.".format(arg.infile))
# Output dir
sanity.file_checker(
arg.outpath, "Output argument '{}' is pointing to an "
"existing file. This argument requires a "
"directory.".format(arg.outpath), False)
# Number of Ks
if isinstance(arg.Ks, int):
Ks = range(1, arg.Ks + 1)
else:
Ks = arg.Ks
# Number of replicates
replicates = range(1, arg.replicates + 1)
threads = sanity.cpu_checker(arg.threads)
signal.signal(signal.SIGINT, gracious_exit)
structure_threader(Ks, replicates, threads, wrapped_prog, arg)
if wrapped_prog == "maverick":
bestk = maverick_merger(arg.outpath, Ks, arg.notests)
arg.notests = True
if arg.notests is False:
bestk = structure_harvester(arg.outpath, wrapped_prog)
else:
bestk = Ks
if arg.noplot is False:
create_plts(arg.outpath, wrapped_prog, Ks, bestk, arg)
# Perform only plotting operation
if arg.main_op == "plot":
plots_only(arg)
def main():
"""
Main function, where variables are set and other functions get called
from.
"""
arg = argument_parser(sys.argv[1:])
# Check the existance of several files:
# Popfile
if arg.popfile is not None:
sanity.file_checker(
arg.popfile, "The specified popfile '{}' does not "
"exist.".format(arg.popfile))
# Indfile
if arg.indfile is not None:
sanity.file_checker(
arg.indfile, "The specified indfile '{}' does not "
"exist.".format(arg.indfile))
# Perform usual structure_threader run
if arg.main_op == "run":
# Switch relative to absolute paths
arg.infile = os.path.abspath(arg.infile)
arg.outpath = os.path.abspath(arg.outpath)
# Figure out which program we are wrapping
if "-fs" in sys.argv:
wrapped_prog = "fastStructure"
elif "-mv" in sys.argv:
wrapped_prog = "maverick"
elif "-st" in sys.argv:
wrapped_prog = "structure"
# External program
sanity.file_checker(
arg.external_prog, "Could not find your external program in "
"the specified path "
"'{}'.".format(arg.external_prog))
# Input file
sanity.file_checker(
arg.infile, "The specified infile '{}' does "
"not exist.".format(arg.infile))
# Output dir
sanity.file_checker(
arg.outpath, "Output argument '{}' is pointing to an "
"existing file. This argument requires a "
"directory.".format(arg.outpath), False)
# Number of Ks
if isinstance(arg.Ks, int):
Ks = range(1, arg.Ks + 1)
else:
Ks = arg.Ks
# Number of replicates
replicates = range(1, arg.replicates + 1)
threads = sanity.cpu_checker(arg.threads)
signal.signal(signal.SIGINT, gracious_exit)
structure_threader(Ks, replicates, threads, wrapped_prog, arg)
if wrapped_prog == "maverick":
bestk = maverick_merger(arg.outpath, Ks, arg.notests)
arg.notests = True
if arg.notests is False:
bestk = structure_harvester(arg.outpath, wrapped_prog)
else:
bestk = Ks
if arg.noplot is False:
create_plts(arg.outpath, wrapped_prog, Ks, bestk, arg)
# Perform only plotting operation
if arg.main_op == "plot":
# Get all files matching the provided prefix
if arg.format == "fastStructure":
infiles = [
x for x in os.listdir(".")
if x.startswith(arg.prefix) and x.endswith(".meanQ")
]
elif arg.format == "structure":
infiles = [
x for x in os.listdir(".")
if x.startswith(arg.prefix) and "rep1_" in x
]
else:
infiles = [
x for x in os.listdir(".")
if x.startswith(arg.prefix) and x.endswith(".csv")
]
if not infiles:
print("ERROR: There are no input files that match the"
" provided prefix")
raise SystemExit
if not os.path.exists(arg.outpath):
os.makedirs(arg.outpath)
bestk = [int(x) for x in arg.bestk]
sp.main(infiles,
arg.format,
arg.outpath,
bestk,
popfile=arg.popfile,
indfile=arg.indfile,
filter_k=bestk)
