DUf-ddlZddlZddlmZddlmZmZm Z ddl m Z m Z m Z gdZddZddZdd Zdd Zdd ZddZ ddZ ddZdS)N)checks)_get_default_colnames_verify_columnsis_chrom_dtype)is_complete_ucsc_stringparse_region_stringto_ucsc_string) from_dict from_series from_listfrom_anymake_viewframesanitize_bedframec6|tn|\}}}g}t|D]G\}}|}tj|rd} |} nt d||| | gHtj||||gS)a- Makes a dataframe from a dictionary of {str,int} pairs, interpreted as chromosome names. Note that {str,(int,int)} dictionaries of tuples are no longer supported! Parameters ---------- regions : dict name_col : str 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 ------- df : pandas.DataFrame Nrz"Unsupported dict format: {type(v)}columns) rdictitemsnpisscalar ValueErrorappendpd DataFrame) regionscolsck1sk1ek1datakvchromstartends W/var/www/html/software/conda/lib/python3.11/site-packages/bioframe/core/construction.pyr r s004|)+++MCc DW ##%%))1 ;q>> CECCABB B UE3'(((( <sCo 6 6 66c|tn|\}}}|jj}|||d||ji}tj|S)Nr)rindexvaluesrr)rrrrr chromsr!s r'r r 9sK/3|)+++MCc ] !F agn 5D <  r(namec|tn|\}}}tj|}|jddkr |||g|_n,|jddkr ||||g|_nt d|S)Nrz-wrong number of columns for list input format)rrrshaperr)rname_colrrrr dfs r'r r @s/3|)+++MCc g  B x{a3_ !  3X. HIII Ir(c||tn|\}}}d|D}tj||||g}|S)Nc,g|]}t|S)r .0is r' z)from_ucsc_string_list..Ns! : : :!!$$ : : :r(r)rrr) region_listrrrr parsedr3s r'from_ucsc_string_listr=LsO/3|)+++MCc : :k : : :F fsCo 6 6 6B Ir(Fc8|tn|\}}}t|tjr|||h|jr|}nYt||jj dkrAt||jdr!t||j|||g}ntdt|trt||||g}nt|tjrt!||||g}nt|t"rt%j |dkrt'|g||||g}nFtt%j |dkr0t|dt(rt||||g}nt't+|||||g}nt|t*rt%j |dkrt'|g||||g}ntt%j |dkr0t|dt(rt||||g}n5t'|||||g}ntdt-||rtj||d||< g}t3t|D]h} ||j| -||||j| B|||j| i|||<n#t6$rtd wxYw|S) ae Attempts to make a genomic interval dataframe with columns [chr, start, end, name_col] from a variety of input types. Parameters ---------- regions : supported input Currently supported inputs: - dataframe - series of UCSC strings - dictionary of {str:int} key value pairs - pandas series where the index is interpreted as chromosomes and values are interpreted as end - list of tuples or lists, either [(chrom,start,end)] or [(chrom,start,end,name)] - tuple of tuples or lists, either [(chrom,start,end)] or [(chrom,start,end,name)] fill_null : False or dictionary Accepts a dictionary of {str:int} pairs, interpreted as chromosome sizes. Kept or backwards compatibility. Default False. name_col : str Column name. Only used if 4 column list is provided. Default "name". cols : (str,str,str) Names for dataframe columns. Default None sets them with get_default_colnames(). Returns ------- out_df:dataframe Nrrrz,Unknown dataFrame format: check column names)r/r2rzUnknown input format: z,could not fill ends with provided chromsizes)r isinstancerrissubsetrcopylenr+r1rr=rrr Seriesr tuplerr strlisttype to_numericfillnaranger Exception) r fill_nullr2rrrr out_dfendsr9s r'rrSsH04|)+++MCc'2<((#C c? # #GO 4 4 M\\^^FF'(#*011Q66.s 444!N1%%444r()rrCrzip)reg_dfr2rrrr r3r!s r'add_ucsc_name_columnrUs{04|)+++MCc BBc3((( r#w3C ) )D44t444BxL Ir(c|tn|\}}}t|||}|:t|d|} tj|| dd|st d||jvrM|||j||<n:|dkrt|||}nt dtj |||d r|St d ) a Makes and validates a dataframe `view_df` out of regions. Parameters ---------- regions : supported input type Currently supported input types: - a dictionary where keys are strings and values are integers {str:int}, specifying regions (chrom, 0, end, chrom) - a pandas series of chromosomes lengths with index specifying region names - a list of tuples [(chrom,start,end), ...] or [(chrom,start,end,name), ...] - a pandas DataFrame, skips to validation step name_style : None or "ucsc" If None and no column view_name_col, propagate values from cols[0] If "ucsc" and no column view_name_col, create UCSC style names check_bounds : None, or chromosome sizes provided as any of valid formats above Optional, if provided checks if regions in the view are contained by regions supplied in check_bounds, typically provided as a series of chromosome sizes. Default None. 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 ------- view_df:dataframe satisfying properties of a view Nr@bounds) df_view_col view_name_colrzBInvalid input to make a viewFrame, regions not contained by boundsucsczunknown value for name_styleT)rYr raise_errorsz4could not make valid viewFrame, retry with new input) rrr is_containedrrr+lowerrU is_viewframe) r check_bounds name_stylerYrrrr view_df bounds_dfs r'rrs.V04|)+++MCcwTBBBG\H4HHH "  "    T GO++  %,S\%8GM " "     6 ) )*7]QUVVVGG;<< < }4dQOPPPr(Tc|tn|\}}}|}t||||g|r|j|||g\} } } t | s#||t ||<| tjur| tjus^||tj||<||tj||<tj ||||g d} tj |j | |||gf<|r.| dd|dd||}||||z dk r||||z dkj} |dkr|j | dk}n8|d kr#|j | ||gfj|j | ||gf<nt#d |ddt%j|| r|St#d ) aw Attempts to clean a genomic interval dataframe to be a valid bedframe. Parameters ---------- df1 : pandas.DataFrame recast_dtypes : bool Whether to attempt to recast column dtypes to pandas nullable dtypes. drop_null : bool Drops rows with pd.NA. Default False. start_exceed_end_action : str or None Options: 'flip' or 'drop' or None. Default None. - If 'flip', attempts to sanitize by flipping intervals with start>end. - If 'drop' attempts to sanitize dropping intervals with start>end. - If None, does not alter these intervals if present. 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 ------- out_df : pandas.DataFrame Sanitized dataframe satisfying the properties of a bedframe. Notes ------ The option ``start_exceed_end_action='flip'`` may be useful for gff files with strand information but starts > ends. Nr)axisrT)rdinplace)droprerfflipz+unknown action for intervals with start>endr?zcould not sanitize)rrCrdtypesrastyperGr Int64DtypeisnullanyNAlocdropna reset_indexr]r+rr is_bedframe)df1 recast_dtypes drop_nullstart_exceed_end_actionrrrr rO chrom_dtype start_dtype end_dtype nan_intervalsindss r'rr slV04|)+++MCc XXZZFFS#sO,,,>.4mS#sO.L+ [)k** 2 +,,S11F3K //i2=??6R6R +,,R]__==F3K +,,R]__==F3KIfc3_566:::BBM13FJ}sCo-.4 1d +++d333*"9"?"?"A"A C[6#; &! + 0 0 2 2 8C[6#;.!3;D&&00DAI.(F22/5z$c :J/K/R 4#s+,, !NOOO   D$  7 7 7 &t,,,/ -...r()N)r-N)Fr-N)NNr-N)TFNN)numpyrpandasrrspecsrrr stringopsrr r __all__r r r r=rrUrrr6r(r'rsWIIIIIIIIIISSSSSSSSSS   "7"7"7"7J    XXXXv    " IQIQIQIQ\ N/N/N/N/N/N/r(