DUf:ddlZddlZddlmZddlmZddlmZm Z m Z gdZ dd Z dd Z dd ZddZ ddZddZ ddZ ddZdS)N)ops) construction)_get_default_colnames_verify_column_dtypes_verify_columns) is_bedframe is_catalogedis_overlapping is_viewframe is_contained is_covering is_tiling is_sortedFcp|tn|\}}}t||||gds|rtddSt||||gds|rtddSt j||||g}|d |d zr|rtd dS||||z d kr7|r3td t||||z d kd dSdS)a Checks that required bedframe properties are satisfied for dataframe `df`. This includes: - chrom, start, end columns - columns have valid dtypes - for each interval, if any of chrom, start, end are null, then all are null - all starts < ends. Parameters ---------- df : pandas.DataFrame raise_errors : bool, optional [default: False] If True, raises errors instead of returning a boolean False for invalid properties. cols : (str, str, str) or None The names of columns containing the chromosome, start and end of the genomic intervals, provided separately for each set. The default values are 'chrom', 'start', 'end'. Returns ------- is_bedframe:bool Notes ----- Valid dtypes for chrom are object, string, or categorical. Valid dtypes for start and end are int/Int64Dtype. NTreturn_as_boolz&Invalid bedFrame: Invalid column namesF)colsrz'Invalid bedFrame: Invalid column dtypesr)axiszcInvalid bedFrame: Invalid null values (if any of chrom, start, end are null, then all must be null)rz)Invalid bedframe: starts exceed ends for z intervals) rr TypeErrorrpdisnullanyall ValueErrorsum)df raise_errorsrck1sk1ek1 nan_intervalss Q/var/www/html/software/conda/lib/python3.11/site-packages/bioframe/core/checks.pyr r sL04|)+++MCc 2S#t D D D  FDEE Eu 3S/$ O O O  GEFF FuIb#sC122M   !  $ $ $}'8'8a'8'@'@ @AFFHH  P u C2c7 a$$&&  <3"S')Q.//<<< u 4 view_regionnamec6t||gds|rtd|ddSt||gds|rtd|ddSt||jt||js[|rWt||jt||j}td|dSdS) a} Tests if all region names in `df[df_view_col]` are present in `view_df[view_name_col]`. Parameters ---------- df : pandas.DataFrame view_df : pandas.DataFrame raise_errors : bool If True, raises errors instead of returning a boolean False for invalid properties. Default False. df_view_col: str Name of column from df that indicates region in view. view_name_col: str Name of column from view that specifies region name. Returns ------- is_cataloged:bool Notes ----- Does not check if names in `view_df[view_name_col]` are unique. TrzCould not find `z` column in dfFz Could not find `z#` column in view_dfzIThe following regions in df[df_view_col] not in view_df[view_name_col]: )r rsetcopydropnavaluesissubset difference)rview_dfr df_view_col view_name_colmissing_regionss r$r r Zs\@ 2 }T B B B  MK KKKLL Lu 7]OD I I I  $####$$ $u r+##%%,,..5 6 6 ? ? GM " )**     !"[/"899DDGM*122O?-<?? u 4r%cddlm}|tn|\}}}|||}tj||||z j}tj||||z j}||krdSdS)a Tests if any genomic intervals in a bioframe `df` overlap. Also see :func:`bioframe.ops.merge()`. Parameters ---------- df : pandas.DataFrame cols : (str, str, str) or None The names of columns containing the chromosome, start and end of the genomic intervals, provided separately for each set. The default values are 'chrom', 'start', 'end'. Returns ------- is_overlapping:bool r)mergeNrTF)rr4rnprr,) rrr4r r!r" df_mergedtotal_interval_lentotal_interval_len_mergeds r$r r s(/3|)+++MCcbt$$$IC2c7!2 :;; " #3(G'O P P555tur%c2|tn|\}}}t|||||gds|rtddSt||s|rt ddSt j|jr|rt ddStt||t||jkr|rt d dSt||r|rt d dSdS) a Checks that `region_df` is a valid viewFrame. This includes: - it satisfies requirements for a bedframe, including columns for ('chrom', 'start', 'end') - it has an additional column, view_name_col, with default 'name' - it does not contain null values - entries in the view_name_col are unique. - intervals are non-overlapping Parameters ---------- region_df : pandas.DataFrame Dataframe of genomic intervals to be tested. raise_errors : bool If True, raises errors instead of returning a boolean False for invalid properties. Default False. view_name_col : str Specifies column name of the view regions. Default 'name'. cols : (str, str, str) or None The names of columns containing the chromosome, start and end of the genomic intervals, provided separately for each set. The default values are 'chrom', 'start', 'end'. Returns ------- is_viewframe:bool NTrz"Invalid view: invalid column namesFr5zInvalid view: not a bedframez Invalid view: cannot contain NAszPInvalid view: entries in region_df[view_name_col] must be uniquez-Invalid view: entries must be non-overlapping) rr rr rrisnar,rlenr)r ) region_dfrr1rr r!r"s r$r r sbJ04|)+++MCc Cc=1$     B@AA Au yt , , ,  =;<< <u wy $$&&  A?@@ @u 3y' ( ())C -0H0O,P,PPP  9 uid+++  NLMM Mu 4r%cddlm}|tn|\}} } |tn|\} } } | tj||||}|| dzdksJ|| dzdksJ|| || dzksJ|| || dzksJn"#t$r|rtdYdSwxYwd St|||| s|rtd dS||||||| }tj || j || j k}tj || j || j k}|s|r|rtddSd S) a6 Tests if all genomic intervals in a bioframe `df` are cataloged and do not extend beyond their associated region in the view `view_df`. Parameters ---------- df : pandas.DataFrame view_df : pandas.DataFrame Valid viewframe. raise_errors : bool If True, raises errors instead of returning a boolean False for invalid properties. Default False. df_view_col: Column from df used to associate interviews with view regions. Default `view_region`. view_name_col: Column from view_df with view region names. Default `name`. cols: (str, str, str) Column names for chrom, start, end in df. cols_view: (str, str, str) Column names for chrom, start, end in view_df. Returns ------- is_contained:bool r)trimN)cols1cols2_rzdf not contained in view_dfFT)r0r1zdf not cataloged in view_df)r/r0r1r cols_view) rr?roverlapr;rrAssertionErrorr rr6rr,)rr/rr0r1rrCr?r r!r"ck2sk2ek2df_view_assigneddf_trimis_start_trimmedis_end_trimmeds r$rrsNR/3|)+++MCc/8/@)+++iMCc "{2wd)TTT $S3Y/4466;;==BBBB$S3Y/4466;;==BBBB$S)-=cCi-HHMMOO O O O%S)-=cCi-HHMMOO O O O O    $%BCCCuu   t  GM     <:;; ;ud #  Gvbgn 0CCDDVBsGNgcl.AABBN>  <:;; ;utsCD D*)D*c@ddlm}||||||jrdSdS)a Tests if a view `view_df` is covered by the set of genomic intervals in the bedframe `df`. This test is true if ``complement(df,view_df)`` is empty. Also note this test ignores regions assigned to intervals in `df` since regions are re-assigned in :func:`bioframe.ops.complement`. Parameters ---------- df : pandas.DataFrame view_df : pandas.DataFrame Valid viewFrame. view_name_col: Column from view_df with view region names. Default `name`. cols : (str, str, str) or None The names of columns containing the chromosome, start and end of the genomic intervals, provided separately for each set. The default values are 'chrom', 'start', 'end'. cols_view: (str, str, str) or None The names of columns containing the chromosome, start and end of the genomic intervals in view_df, provided separately for each set. The default values are 'chrom', 'start', 'end'. Returns ------- is_covering:bool r) complement)r/r1rrCTF)rrNempty)rr/r1rrCrNs r$rr[sPF!     z #    tur%ctj|||}t||r|rtddSt |||||s|rtddSt ||||||s|rtddSd S) a Tests if a view `view_df` is tiled by the set of genomic intervals in the bedframe `df`. This is true if: - df is not overlapping - df is covering view_df - df is contained in view_df Parameters ---------- df : pandas.DataFrame view_df : pandas.DataFrame valid viewFrame raise_errors : bool If True, raises errors instead of returning a boolean False for invalid properties. Default False. df_view_col: str Name of column from df that indicates region in view. view_name_col: str Name of column from view that specifies unique region name. cols : (str, str, str) or None The names of columns containing the chromosome, start and end of the genomic intervals, provided separately for each set. The default values are 'chrom', 'start', 'end'. cols_view: (str, str, str) or None The names of columns containing the chromosome, start and end of the genomic intervals in view_df, provided separately for each set. The default values are 'chrom', 'start', 'end'. Returns ------- is_tiling:bool )r1rr5overlapsF)r1rrCz not covered)r0r1rrCz not containedT)rmake_viewframer rrr)rr/rr0r1rrCs r$rrsh)}9Gbt$$$  )Z(( (u  G=ty     ,]++ +u  #        ._-- -u 4r%Tc ddlm}||||||||}||rdSdS)a> Tests if a bedframe is changed by sorting. Also see :func:`bioframe.ops.sort_bedframe`. Parameters ---------- df : pandas.DataFrame view_df : pandas.DataFrame | dict-like Optional view to pass to ``sort_bedframe``. When it is dict-like :func:'bioframe.make_viewframe' will be used to convert to viewframe. If view_df is not provided df is assumed to be sorted by chrom and start. reset_index : bool Optional argument to pass to ``sort_bedframe``. df_view_col: None | str Name of column from df that indicates region in view. If None, :func:'bioframe.assign_view' will be used to assign view regions. Default None. view_name_col: str Name of column from view that specifies unique region name. cols : (str, str, str) or None The names of columns containing the chromosome, start and end of the genomic intervals, provided separately for each set. The default values are 'chrom', 'start', 'end'. cols_view: (str, str, str) or None The names of columns containing the chromosome, start and end of the genomic intervals in view_df, provided separately for each set. The default values are 'chrom', 'start', 'end'. Returns ------- is_sorted : bool r) sort_bedframe)r/ reset_indexr0r1rrCTF)rrTr*equals) rr/rUr0r1rrCrT df_sorteds r$rrsjf$#####   # I yytur%)FN)Fr&r')N)Fr'N)FNr'NN)r'NN)Fr&r'NN)NTNr'NN)numpyr6pandasrrrspecsrrr __all__r r r r rrrrr%r$r^s|PPPPPPPPPP    CCCCNOU9999x    FEEEEV WWWWt....h MMMMd  BBBBBBr%