Source code for pyGenClean.SampleMissingness.sample_missingness
#!/usr/bin/env python2.7
# This file is part of pyGenClean.
#
# pyGenClean is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
#
# pyGenClean is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with
# pyGenClean. If not, see <http://www.gnu.org/licenses/>.
import os
import sys
import logging
import argparse
import subprocess
from .. import __version__
logger = logging.getLogger("sample_missingness")
[docs]def main(argString=None):
"""The main function of the module.
:param argString: the options.
:type argString: list
These are the steps:
1. Prints the options.
2. Runs Plink with the ``mind`` option (:py:func:`runPlink`).
"""
# Getting and checking the options
args = parseArgs(argString)
checkArgs(args)
logger.info("Options used:")
for key, value in vars(args).iteritems():
logger.info(" --{} {}".format(key.replace("_", "-"), value))
# Running Plink
logger.info("Running Plink")
runPlink(args)
[docs]def runPlink(options):
"""Run Plink with the ``mind`` option.
:param options: the options.
:type options: argparse.Namespace
"""
# The plink command
plinkCommand = [
"plink",
"--noweb",
"--bfile" if options.is_bfile else "--tfile",
options.ifile,
"--mind",
str(options.mind),
"--make-bed",
"--out",
options.out,
]
output = None
try:
output = subprocess.check_output(plinkCommand,
stderr=subprocess.STDOUT, shell=False)
except subprocess.CalledProcessError:
msg = "plink: couldn't run plink"
raise ProgramError(msg)
[docs]def checkArgs(args):
"""Checks the arguments and options.
:param args: a object containing the options of the program.
:type args: argparse.Namespace
:returns: ``True`` if everything was OK.
If there is a problem with an option, an exception is raised using the
:py:class:`ProgramError` class, a message is printed to the
:class:`sys.stderr` and the program exists with code 1.
"""
# Check if we have the tped and the tfam files
required_file_extensions = {".tfam", ".tped"}
if args.is_bfile:
required_file_extensions = {".bed", ".bim", ".fam"}
for fileName in [args.ifile + i for i in required_file_extensions]:
if not os.path.isfile(fileName):
msg = "{}: no such file".format(fileName)
raise ProgramError(msg)
# Check the mind option (between 0 and 1, inclusive)
if (args.mind < 0) or (args.mind > 1):
msg = "mind=%f: must be between 0 and 1 (inclusive)" % args.mind
raise ProgramError(msg)
return True
[docs]def parseArgs(argString=None): # pragma: no cover
"""Parses the command line options and arguments.
:param argString: the options.
:type argString: list
:returns: A :py:class:`argparse.Namespace` object created by the
:py:mod:`argparse` module. It contains the values of the
different options.
============== ====== =====================================================
Options Type Description
============== ====== =====================================================
``--ifile`` string The input file prefix (either a Plink binary file or
a tfile).
``--is-bfile`` bool The input file (``--ifile``) is a bfile instead of a
tfile.
``--mind`` float The missingness threshold.
``--out`` string The prefix of the output files.
============== ====== =====================================================
.. note::
No option check is done here (except for the one automatically done by
argparse). Those need to be done elsewhere (see :py:func:`checkArgs`).
"""
args = None
if argString is None:
args = parser.parse_args()
else:
args = parser.parse_args(argString)
return args
[docs]class ProgramError(Exception):
"""An :py:class:`Exception` raised in case of a problem.
:param msg: the message to print to the user before exiting.
:type msg: str
"""
def __init__(self, msg):
"""Construction of the :py:class:`ProgramError` class.
:param msg: the message to print to the user
:type msg: str
"""
self.message = str(msg)
def __str__(self):
return self.message
# The parser object
pretty_name = "Sample missingness"
desc = "Computes sample missingness using Plink."
long_desc = ("The script identifies poorly performing DNA samples with a "
r"genome-wide genotyping success rate $<{success_rate}$\%.")
parser = argparse.ArgumentParser(description=desc)
parser.add_argument("-v", "--version", action="version",
version="pyGenClean version {}".format(__version__))
# The INPUT files
group = parser.add_argument_group("Input File")
group.add_argument("--ifile", type=str, metavar="FILE", required=True,
help=("The input file prefix (by default, this input file "
"must be a tfile. If options --is-bfile is used, the "
"input file must be a bfile)."))
# The options
group = parser.add_argument_group("Options")
group.add_argument("--is-bfile", action="store_true",
help=("The input file (--ifile) is a bfile instead of a "
"tfile."))
group.add_argument("--mind", type=float, metavar="FLOAT", default=0.1,
help=("The missingness threshold (remove samples with "
"more than x percent missing genotypes). [Default: "
"%(default).3f]"))
# The OUTPUT files
group = parser.add_argument_group("Output File")
group.add_argument("--out", type=str, metavar="FILE", default="clean_mind",
help=("The prefix of the output files (wich will be a "
"Plink binary file). [default: %(default)s]"))
[docs]def safe_main():
"""A safe version of the main function (that catches ProgramError)."""
try:
main()
except KeyboardInterrupt:
logger.info("Cancelled by user")
sys.exit(0)
except ProgramError as e:
logger.error(e.message)
parser.error(e.message)
if __name__ == "__main__":
safe_main()
