Source code for pacbio_data_processing.ui.cl

#######################################################################
#
# Copyright (C) 2021, 2022 David Palao
#
# This file is part of PacBio data processing.
#
#  PacBioDataProcessing 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.
#
#  PacBio data processing 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 PacBioDataProcessing. If not, see <http://www.gnu.org/licenses/>.
#
#######################################################################

"""This module defines the functions to collect user input from the
command line."""

import argparse

from .options import SM_ANALYSIS_OPTS, BAM_FILTER_OPTS
from .common import parse_user_input
from ..constants import (
    SM_ANALYSIS_EXE, SM_ANALYSIS_DESC, BAM_FILTER_EXE, BAM_FILTER_DESC,
)


# def old_parse_cl():
#     parser.add_argument(
#         "-r", "--restart-from-old-dir", metavar="DIR", type=Path,
#         help=(
#             "continue analysis from a previous (unfinished) one; "
#             "%(metavar)s must be the temporary directory remaining from "
#             "the old run."
#         )
#     )


[docs]def parse_cl_sm_analysis(): return parse_user_input( argparse.ArgumentParser, SM_ANALYSIS_EXE, SM_ANALYSIS_DESC, SM_ANALYSIS_OPTS )
[docs]def parse_cl_bam_filter(): return parse_user_input( argparse.ArgumentParser, BAM_FILTER_EXE, BAM_FILTER_DESC, BAM_FILTER_OPTS )