DUf2PddlZddlZddlZddlZddlZddlZddlmZmZm Z m Z m Z m Z ddl mZddlmZmZmZmZmZmZmZmZmZddl mZddlmZddl mZdd l mZdd lmZdd lm Z m!Z!m"Z"dd lm#Z#dd l m$Z$ddl%m%Z%m&Z&gdZ'dZ(dZ)dZ*dZ+ej,ee+e*dZ-dS)N)Interval IntervalFileoverlap AttributesMalformedBedLineErrorIntervalIterator)contrib) get_tempdir set_tempdircleanup find_taggedset_bedtools_path chromsizesget_chromsizes_from_ucscchromsizes_to_filecreate_interval_from_list)helpers)BedTool)genome_registry)stats) __version__)data_direxample_filenamelist_example_files)example_bedtool)settings)loggerch)za.bed.zb.bedztest.faza.bamc^|rVtjtjt jtjd}d}tjddStjtjt jtjd}d}tjddS)aZ 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. Tz~Debug mode enabled. You may also want to set pybedtools.KEEP_TEMPFILES=True to prevent automatic deletion of files upon exit.FzDebug mode disabledN)rsetLevelloggingDEBUGrinfoINFO)x_DEBUGKEEP_TEMPFILESs P/var/www/html/software/conda/lib/python3.11/site-packages/pybedtools/__init__.py debug_moder**s + &&& GM"""  "      %%% GL!!! )*****c$tj|i|S)zO For backwards compatibility; please use helpers._check_for_bedtools() )r_check_for_bedtools)argskwargss r)check_for_bedtoolsr0Gs  & 7 7 77r+c:tt|SN)rlist)fieldss r)interval_constructorr5Ps $T&\\ 2 22r+c:tt|jffSr2)r5tupler4)intervals r)interval_reducerr9Ts %"8"8!: ::r+cttjtjtjtj}t |trKt|D])\}} ||}||#t$rY&wxYwt |trddl }| }| ||dgkrtdt|D]9\}} |d|}||(#|j$rY4wxYwdSdS)a 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. )bedtoolsrtabixbgziprNpathsz;Invalid path config -- must have only one section, [paths].)dictrr set_R_pathset_tabix_pathset_bgzip_path isinstancer3itemsKeyErrorstr configparserSafeConfigParserreadsections ValueErrorget NoOptionError)fnsettersprogsetterpathrHcs r)load_path_configrU[s0*  $$ G"d 11  LD& $xt     "c  ) ) + + r ::<rcs@                        EEEEEEEEEE$$$$$$777 +++:888333;;;x)+?@@@66666r+