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import os
import sys
import subprocess
import tempfile
import logging
from six.moves import urllib
from six.moves import copyreg
from .cbedtools import (
Interval,
IntervalFile,
overlap,
Attributes,
MalformedBedLineError,
IntervalIterator,
)
from . import contrib
from .helpers import (
get_tempdir,
set_tempdir,
cleanup,
find_tagged,
set_bedtools_path,
chromsizes,
get_chromsizes_from_ucsc,
chromsizes_to_file,
create_interval_from_list,
)
from . import helpers
from .bedtool import BedTool
from . import genome_registry
from . import stats
from .version import __version__
from .filenames import data_dir, example_filename, list_example_files
from .bedtool import example_bedtool
from . import settings
from .logger import logger, ch
example_files = ["a.bed.", "b.bed", "test.fa", "a.bam"]
def debug_mode(x):
"""
Enable debug mode.
Use debug_mode(True) to show debug log events in the console and to save
calling info in BedTool objects, and turn it off again with
debug_mode(False).
Note that `pybedtools.KEEP_TEMPFILES` will be set as well, so you will need
to clean up the tempfile directory manually after using debug mode.
"""
if x:
logger.setLevel(logging.DEBUG)
ch.setLevel(logging.DEBUG)
_DEBUG = True
KEEP_TEMPFILES = True
logger.info(
"Debug mode enabled. You may also want to set "
"pybedtools.KEEP_TEMPFILES=True to prevent automatic deletion "
"of files upon exit."
)
else:
logger.setLevel(logging.INFO)
ch.setLevel(logging.INFO)
_DEBUG = False
KEEP_TEMPFILES = False
logger.info("Debug mode disabled")
def check_for_bedtools(*args, **kwargs):
"""
For backwards compatibility; please use helpers._check_for_bedtools()
"""
return helpers._check_for_bedtools(*args, **kwargs)
# Allow Interval objects to be pickled -- required if you want to pass them
# across process boundaries
def interval_constructor(fields):
return create_interval_from_list(list(fields))
def interval_reducer(interval):
return interval_constructor, (tuple(interval.fields),)
copyreg.pickle(Interval, interval_reducer, interval_constructor)
def load_path_config(fn):
"""
You can use a config file to specify installation paths of various programs
used by pybedtools. This can be useful for testing, or using different
versions of programs.
`fn` is a config file with the following format. If an entry is blank,
then assume it's already on the path. All items must be lowercase::
[paths]
bedtools=/tools/BEDTools/bin
r=
tabix=
bgzip=
You only need to specify paths you need to change, so this is a valid file
that will only specify the path to use for R::
[paths]
r=/usr/bin/R-dev
If `fn` is not a string, then assume it is a dictionary of (program,
paths). This is used primarily for testing.
"""
setters = dict(
bedtools=helpers.set_bedtools_path,
r=helpers.set_R_path,
tabix=helpers.set_tabix_path,
bgzip=helpers.set_bgzip_path,
)
if isinstance(fn, dict):
for prog, setter in list(setters.items()):
try:
path = fn[prog]
setter(path)
except KeyError:
pass
if isinstance(fn, str):
from six.moves import configparser
c = configparser.SafeConfigParser()
c.read(fn)
if c.sections() != ["paths"]:
raise ValueError(
"Invalid path config -- must have " "only one section, [paths]."
)
for prog, setter in list(setters.items()):
try:
path = c.get("paths", prog)
setter(path)
except configparser.NoOptionError:
pass
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