o NrfZ2@sddlZddlZddlZddlZddlmmZddl m Z m Z ddl m Z ddZ dddZdd Zd d Zd d Z    dddZdddZ    dddZdS)N)est_query_size_ixload_bai_index) abs2genomicc Csg}d}|j}|j}|j|j}|D]x}|dtjkr.|||d|df||d7}q|dtjkrB|||d|dfq|dtjkr\|||d|df||d7}q|dtjkrv|||d|df||d7}q|dtj ks|dtj kr||d7}qt |r|d}|d}|dtj kr|||dd|df|dtj kr|||dd |df|dtj kr|||dd|df|dtj kr||d |df|S) NrXIDNSH) cigartuplespos query_lengthpysamZCDIFFappendZCINSZCDELZ CREF_SKIPZCEQUALZCMATCHlenZ CSOFT_CLIPZ CHARD_CLIP) readsubscurr_posr Z readstartZreadendZctupleZ first_ctupleZ last_ctuplerZ/var/www/html/software/conda/envs/catlas/lib/python3.10/site-packages/clodius/tiles/bam.pyget_cigar_substitutions s@  rc s|durg}|D] \}}||t|gg7}q nt|j} t|j} t| } tt | dd| D}dd|D} tj dt | f} idgdgdgd gd gd gd gd gdgdgdgdgdgdgdgdg} ddd} t |}d}t | ||D]\}|t||7}qd}||krddiSt | ||D]6\}t| |}|t|krq||d}||}|D]jrqzd}jrjrd}jrd}j|}| d|g7<| dtj|g7<| dtj|g7<| d jg7<| d |g7<| d jg7<| djg7<jdk}|rCt||}nd}|sjr~zfd djd!d!d"D}Wn tyjg}Ynw|rtt |||| d|g7<n| dg7<n | d|g7<| dt!g7<t"j#}| d|$d#dg7<| d| j%g7<Wnz| d &d$g7<Wqt'y| d dg7<Yqwq| S)%a Sample reads from the specified region, assuming that the chromosomes are ordered in some fashion. Returns an list of pysam reads Parameters: ----------- samfile: pysam.AlignmentFile A pysam entry into an indexed bam file start_pos: int The start position of the sampled region end_pos: int The end position of the sampled region chromsize: pandas.Series A listing of chromosome sizes. If not provided, the chromosome list will be extracted from the the bam file header cache: An object that implements the `get`, `set` and `exists` methods for caching data Returns ------- reads: [read1, read2...] The list of in the sampled regions NcSg|]}t|qSrint.0lengthrrr ^zload_reads..cSg|]}|dqSrrrrrrrr`r ridfromtomdZchrNameZ chrOffsetZcigarZm1FromZm1ToZm2FromZm2Tomapqztags.HPZstrandvariantsZcigars-+)TFgNAerrorz,Tile encompasses too much data: {total_size}Z_1Z_2i@cs\g|]*}|dkrkr,nn|ddur|dr|d|dj|dfqS)rNr)islowerquery_sequencer#endrstartrrrs  T)Zwith_seqZ matches_onlyZHPZMD)(itemsrnparray referenceslengthsctbw natsortedlistzipZr_ZcumsumrrrrfetchZ is_unmappedZ is_pairedZis_read1Zis_read2Z query_nameZreference_startZ reference_endZreference_nameZ cigarstringr)rget_cached_variantsr1Zget_aligned_pairs ValueErrorset_cached_variantsrdicttagsgetZ is_reverseZget_tagKeyError)samfile start_posend_pos chromsizesindex_filenamecachechromsizes_listchromsizer8r9Zabs_chrom_offsetsresultsZstrandsidx total_sizeZcidZMAX_SIZEZ chr_offsetZseq_nameZreadsZ id_suffixread_idZ use_cacher*rCrr2r load_reads4s                   YrScCs,d|}|r||rt||SdS)zTry to get variants from a read we've seen before. This is useful for ONT reads where there's many variants per read and retrieving them takes a while. variants.N)existsjsonloadsrD)rKrRcache_idrrrr?s r?cCs(d|}|r||t|dSdS)z$Save a set of variants to the cache.rTN)setrVdumps)rKrRr*rXrrrrAs rAc s|dur"g}|D] \}}||t|gg7}q tdd|D}n2t|j}t|j}t|j}tt||t |}fdd|D}t t|dd|D}d}t t ||t d} d} d g|g|d| ||| | d } | S) at Get the tileset info for a bam file Parameters ---------- tileset: tilesets.models.Tileset object The tileset that the tile ids should be retrieved from Returns ------- tileset_info: {'min_pos': [], 'max_pos': [], 'tile_size': 1024, 'max_zoom': 7 } NcSr!r"r)rcrrrrr z*alignment_tileset_info..csg|]}|qSrrr#Z ref_lengthsrrrr cSrrrrrrrrr r/ir)Zmin_posZmax_pos max_width tile_sizerImax_zoommax_tile_width)r5rsumr9r6r7r8rBr=r:r;r<mathceillog) rFrIrLrMrN total_lengthr8r9r_r`ZMAX_TILE_WIDTH tileset_inforr\ralignment_tileset_infos0      rhc Csg}t||}|D]R}|ddd} ttt| dd} |ddt| d} |r>| |kr>|dd |ifgSt| d| } | | } t|| | |||d }|||fg7}q |S) a Generate tiles from a bigwig file. Parameters ---------- tileset: tilesets.models.Tileset object The tileset that the tile ids should be retrieved from tile_ids: [str,...] A list of tile_ids (e.g. xyx.0.0) identifying the tiles to be retrieved index_filename: str The name of the file containing the index max_tile_width: int How wide can each tile be before we return no data. This can be used to limit the amount of data returned. cache: An object that implements the `get`, `set` and `exists` methods for caching data Returns ------- tile_list: [(tile_id, tile_data),...] A list of tile_id, tile_data tuples |r.rr^r/r-z1Tile too large, no data returned. Max tile size: )rGrHrIrJrK)rhsplitr<maprrS)rFtile_idsrJrIrarKZgenerated_tilesZtsinfoZtile_idZ tile_id_partsZ tile_positionZ tile_widthrGrHZ tile_valuerrralignment_tiles3s0    rocCst|}t||SN)r AlignmentFilerh)filenamerIrFrrrrgvs  rgcCs0|s|d}tj||d}t||||d|dS)Nz.bai)rJ)rJrIrarK)rrqro)rrrnrJrIrarKrFrrrtiles|s rs)NNN)NNNNrp)rVrcnumpyr6rZclodius.tiles.bigwigrsZbigwigr:Zclodius.tiles.tabixrrZclodius.tiles.utilsrrrSr?rArhrorgrrrrs2 ) 5 : C