# -*- coding: utf-8 -*-
"""
pairtools
~~~~~~~~~
CLI tools to process mapped Hi-C data
:copyright: (c) 2017-2019 Massachusetts Institute of Technology
:author: Mirny Lab
:license: MIT
"""
__version__ = '0.3.0'
import click
import functools
import sys
CONTEXT_SETTINGS = {
'help_option_names': ['-h', '--help'],
}
@click.version_option(version=__version__)
@click.group(context_settings=CONTEXT_SETTINGS)
@click.option(
'--post-mortem',
help="Post mortem debugging",
is_flag=True,
default=False
)
@click.option(
'--output-profile',
help="Profile performance with Python cProfile and dump the statistics "
"into a binary file",
type=str,
default=''
)
def cli(post_mortem, output_profile):
'''Flexible tools for Hi-C data processing.
All pairtools have a few common options, which should be typed _before_
the command name.
'''
if post_mortem:
import traceback
try:
import ipdb as pdb
except ImportError:
import pdb
def _excepthook(exc_type, value, tb):
traceback.print_exception(exc_type, value, tb)
print()
pdb.pm()
sys.excepthook = _excepthook
if output_profile:
import cProfile
import atexit
pr = cProfile.Profile()
pr.enable()
def _atexit_profile_hook():
pr.disable()
pr.dump_stats(output_profile)
atexit.register(_atexit_profile_hook)
def common_io_options(func):
@click.option(
'--nproc-in',
type=int,
default=3,
show_default=True,
help='Number of processes used by the auto-guessed input decompressing command.'
)
@click.option(
'--nproc-out',
type=int,
default=8,
show_default=True,
help='Number of processes used by the auto-guessed output compressing command.'
)
@click.option(
'--cmd-in',
type=str,
default=None,
help='A command to decompress the input file. '
'If provided, fully overrides the auto-guessed command. '
'Does not work with stdin. '
'Must read input from stdin and print output into stdout. '
'EXAMPLE: pbgzip -dc -n 3'
)
@click.option(
'--cmd-out',
type=str,
default=None,
help='A command to compress the output file. '
'If provided, fully overrides the auto-guessed command. '
'Does not work with stdout. '
'Must read input from stdin and print output into stdout. '
'EXAMPLE: pbgzip -c -n 8'
)
@functools.wraps(func)
def wrapper(*args, **kwargs):
return func(*args, **kwargs)
return wrapper
from .pairtools_dedup import dedup
from .pairtools_sort import sort
from .pairtools_flip import flip
from .pairtools_merge import merge
from .pairtools_markasdup import markasdup
from .pairtools_select import select
from .pairtools_split import split
from .pairtools_restrict import restrict
from .pairtools_phase import phase
from .pairtools_parse import parse, parse_cigar, parse_algn
from .pairtools_stats import stats
from .pairtools_sample import sample
from .pairtools_filterbycov import filterbycov
