Ri@dZddlZddlZddlZddlZddlZddlZddlmZddlm Z ddl Z ddl m Z ddl mZddlmZddlmZed d ZGd d eZed deddd eddd eddd eddd eddd eddd eddd edd d! edd"d# ed$d%d& ed'd(d) ed'd*d+ g e_Gd,d-ej.ZGd.d/ej0ZGd0d1ejZGd2d3ZGd4d5eZGd6d7ZGd8d9ZGd:d;eZGd<d=ZGd>d?eZ Gd@dAZ!GdBdCZ"GdDdEe!Z#GdFdGZ$GdHdIZ%GdJdKZ&GdLdMZ'GdNdOZ(GdPdQZ)y)RaBio.Align support for alignment files in the bigBed format. The bigBed format stores a series of pairwise alignments in a single indexed binary file. Typically they are used for transcript to genome alignments. As in the BED format, the alignment positions and alignment scores are stored, but the aligned sequences are not. See http://genome.ucsc.edu/goldenPath/help/bigBed.html for more information. You are expected to use this module via the Bio.Align functions. N) namedtuple)BytesIO) Alignment) interfaces)Seq) SeqRecordField)as_typenamecommentc`eZdZUdZded<dZedZedZdZ dZ fdZ xZ S) AutoSQLTablezJAutoSQL table describing the columns of an (possibly extended) BED format.defaultc*||_||_||ddy)zKCreate an AutoSQL table describing the columns of an (extended) BED format.N)r r )selfr r fieldss H/home/agent/.friday_env/lib/python3.12/site-packages/Bio/Align/bigbed.py__init__zAutoSQLTable.__init__Ms  Qcj|jdsJ|ddj}|jdd\}}|dk(sJ|jdd\}}|jdsJ|j dd}|d|}||dzdj }|jdsJ|jdsJ|ddj }g}|r|j d}|j d|dz}||dz|} |d|j } | jd sJ| ddjdd\} } | jd r| j d }| d|} n| } | d vsJt| | | }|j|||dzdj }|rt|||S) z?Return an AutoSQLTable initialized using the bytes object data.Ntable"();][) intuintshortushortbyteubytefloatcharstringlstring) endswithdecodesplit startswithfindstripindexrsplitr appendr)clsdatatextwordr ir rj field_comment definition field_type field_name data_typefields r from_byteszAutoSQLTable.from_bytesSs}}U###CRy!ZZa( dwZZa( ds### IIc1 q)AEG}""$s###}}S!!!Abz! 3A 3A&A QOMbq)J&&s+ ++%/_%;%;D!%D "J ""3'$$S)&rN &  !   *j-@E MM% A=&&(D56D'622rcF|j|jdzS)z@Return an AutoSQLTable initialized using the string object data.r)r@encode)r4r5s r from_stringzAutoSQLTable.from_strings~~dkkme344rctd|D}td|Ddz}g}|jd|jz|jd|jz|jd|D]C}|jdz}|jd|d |d |j||jfzE|jd d j |S) Nc3XK|]"}tt|j$ywN)lenstrr .0r?s r z'AutoSQLTable.__str__..sCUS/0Cs(*c3FK|]}t|jywrF)rGr rIs rrKz'AutoSQLTable.__str__..s;UUZZ;s!rz table %s z"%s" z( rz %-zs %-z s "%s" z) )maxr3r r r join)r type_width name_widthlinesr?r s r__str__zAutoSQLTable.__str__sCdCC ;d;;a?  \DII-. X ,- U E::#D LL |4 |;?MMMM    Uwwu~rc:t|jdzS)Nr)rHrBrs r __bytes__zAutoSQLTable.__bytes__s4y!E))rct|tr0t| |}t |j |j |St| |SrF) isinstanceslicesuper __getitem__rr r )rr8r __class__s rr[zAutoSQLTable.__getitem__sC a W(+F 4<<@ @7&q) )r) __name__ __module__ __qualname____doc____annotations__r classmethodr@rCrSrVr[ __classcell__r\s@rrrHsNT  *3*3X55(***rrbedzBrowser Extensible Datar)chromz)Reference sequence chromosome or scaffoldr" chromStartzStart position in chromosomechromEndzEnd position in chromosomer z Name of item.scorezScore (0-1000)zchar[1]strandz+ or - for strand thickStartz4Start of where display should be thick (start codon)thickEndz1End of where display should be thick (stop codon)reservedz Used as itemRgb as of 2004-11-22r! blockCountzNumber of blockszint[blockCount] blockSizesz#Comma separated list of block sizes chromStartsz&Start positions relative to chromStartcXeZdZdZdZdZ d fd ZdZdZdZ dZ d Z xZ S) AlignmentWriterz1Alignment file writer for the bigBed file format.bigBedbc |dks|dkDr tdt | |||_||_||_||_||_||_||_ y)aCreate an AlignmentWriter object. Arguments: - target - output stream or file name. - bedN - number of columns in the BED file. This must be between 3 and 12; default value is 12. - declaration - an AutoSQLTable object declaring the fields in the BED file. Required only if the BED file contains extra (custom) fields. Default value is None. - targets - A list of SeqRecord objects with the chromosomes in the order as they appear in the alignments. The sequence contents in each SeqRecord may be undefined, but the sequence length must be defined, as in this example: SeqRecord(Seq(None, length=248956422), id="chr1") If targets is None (the default value), the alignments must have an attribute .targets providing the list of SeqRecord objects. - compress - If True (default), compress data using zlib. If False, do not compress data. Use compress=False for faster searching. - blockSize - Number of items to bundle in r-tree. See UCSC's bedToBigBed program for more information. Default value is 256. - itemsPerSlot - Number of data points bundled at lowest level. See UCSC's bedToBigBed program for more information. Use itemsPerSlot=1 for faster searching. Default value is 512. - extraIndex - List of strings with the names of extra columns to be indexed. Default value is an empty list.  zbedN must be between 3 and 12N) ValueErrorrZrbedN declarationtargetscompressextraIndexNames itemsPerSlot blockSize) rtargetryrzr{r|r~r extraIndexr\s rrzAlignmentWriter.__init__s`^ !8tby<= =   &   )("rc  |j |j}n |j}t}|j|_|j |jd|j|_|j}t||_ t|j|}|j|||\}}|jt|j|jtt j|j#|_|jt||j#|_|jtt(j|j#|_|jt|j|j#|_t/j|t1|j2t|||j#|_t j7|} |jt|j9dt:j<|j?t||jA||| |\} } |jBr-tE| |jFtHjz|_%nd|_%|j#|_&tOj| |j2d|jL||jQ|||jL|j4z || \} } t| |_)|D]`}|j#|_*|jVjYt/j|jV|j2|b|j[d|jt||jt| |j[|j&|jt| |j*|j#k(sJ|j]||j[dt^j`|jbj9dt:j<}|j|y#t $r&t jd|j|_YwwxYw)zWrite the alignments to the file stream, and return the number of alignments. alignments - A list or iterator returning Alignment objects stream - Output file stream. Nrr)2r{_HeaderrydefinedFieldCountrzAttributeErrorrrrG fieldCount _ExtraIndicesr}_get_chrom_usagewritebytessize _ZoomLevelstell autoSqlOffsettotalSummaryOffset_SummaryextraIndicesOffsetchromosomeTreeOffset_BPlusTreeFormatterminrfullDataOffsetcalculate_reductionsto_bytessys byteorder initializewrite_alignmentsr|rNr~_RegionSummaryuncompressBufSizefullIndexOffset_RTreeFormatter_write_zoom_levels zoomLevels fileOffsetchunkssortseektofileioSEEK_END signature)rstream alignmentsr{headerrz extra_indiceschromUsageListaveSize reductions maxBlockSizeregionszoomListtotalSum extra_indexr5s r write_filezAlignmentWriter.write_files <<  ((GllG#'99    # E#-#9#9+DII#F &&  ,%d&:&:KH "&"7"7 #   U6;;'( U;++,-%{{} U;'($*KKM! U8==)*$*KKM! U=--./&,kkm### CN0CDf !'  55g>  S_--a?@  Z1 $ 5 5     !  g =='*d//.2E2EE(F $()F $!' T^^Q(>(> "44    " "V%:%: :    ( M( TK%+[[]K "    # # %  ! ' ' (:(:DNNF S T  A U6]# U8_% F--. U8_%((FKKM999V$ Ar{{#((CMM: T{" E#/#7#7 $))#D  EsR55+S$#S$c `d}d}d}d}d}g} d} d} tj} |D]?} | jdj}| jd}| jd}|D]}|j | ||kDrt d|d|d|d |d z }|||z z }||k7r}||kDrt d |d |r| j||| f|d z }|D]}|j|k(snt d |d |d |}t| t|} t|} d}|| kDrt d|d|d| d|d dk\r ||z }|| kr|dkrt d|d |} |}B|r| j||| ftj| dd| fddg} |dkDr||z }||_ | |fS)NrrMrrrrrzend (z) before start (z) in alignment [rrz7alignments are not sorted by target name at alignment [zfailed to find target 'z' in target list at alignment [zend coordinate z bigger than z size of z at alignment [z]'z(alignments are not sorted at alignment [r S)id=i4rrdtype) rmaxsize sequencesr coordinatesupdateMaxFieldSizerxr3rNrGnparray_len)r4rr{rrchromId totalBasesbedCountr rkeySize chromSizeminDiff alignmentrfstartendrr lastStartdiffs rrz AlignmentWriter._get_chrom_usagefsx  ++#- I''*--E))$/E''.C, : ..y9 :s{ C5 07GzQRS MH #+ %Ju}%<$QRZQ[[\]"))4)*DEqLG%FyyE)%1%8WX`Waabcgs5z2K  Y %cU-wi {RabjakkmnA~y('>ax(FxjPQR#GI[- \   ! !4)"< = ayM*M?K  a< 8+G" w&&rct}t}t|dk(rd|_d|_||fS|j }|j } |j} |dz } |j|d_ |D]&} | dtjz} | r| dz} | | ks&n|d} | dj|| tjz}| r t||}n t||}g}g}tj!||}t#| d}|tj$z}|D]}t&j( }|j+||}|D]n}|j-||j/|||z|j0kr3t3j2|}|j4}|j/|j|z }p|j7t|| dk(sJ| d|d_|j}||d_t=j-||| ||| r t||}nt|tj}|j?|| ||| ||fS)Nrrscale) rrrGminValmaxValrr|r~r dataOffsetrrr_ZippedBufferedStream_BufferedStream _RangeTreegenerater!bbiResIncrementrrgenerate_summariesrr3rcopyrflushreductionLevel indexOffsetrreduce)rroutputdataSizerrrrr doCompressr~maxReducedSizeinitialReduction reducedSizerbufferr rezoomedListtreesrdoubleReductionSizetreer summariessummaryrezoomedrs rrz"AlignmentWriter._write_zoom_levelss|=: z?a !HO!HOj!!gIJ,,L%\N%+[[]HQK "$. 1 .v69L9LL 1$K.0  1$.a= V $ + +F 3."5"55D.vt<(6GL'' CE(12E"'+*E*E"E  ,  33E8D (,GLL)NN7+22W[[@#'99W#5 ($++H5 G+, , LLNw<#3F#;; ;;)9')BHQK & ++-K&1HQK #   # #L+v .vt<(1D1DE OO. < !!rc  |j}g}|jj}t|dk\rt d|dt|dkr t d|j d}|j d}||krt d|d |d |d kDrL|j j}|d k(rd }nt|dkDrt d|d|j||dkDrB |j}|dks|dkDrt d|dt|}|j||dkDr5|j d|j dkrd} nd} |j| |dkDr' |j} |jt| |dkDr |j} |  krt d| d| d | dk7r$| |ks| |kDrt dd|d|d | d| | dk7r$| |ks| |kDrt d!d|d|d | d| |jt| |d"kDr |j} | jd#jd#} t| d k(rt!d$| Drn'dt#| cxkrd%krnnnt d&| d'|j| |d(kDrjt%j&|j }t)|dk7dd)k(}|j+d|}t|}|jt||d*kDr*|jd#j-d+Dd#z|d,kDrC|j ddd-f|z }|jd#j-d.|Dd#z|d/kDr|d0k7rt d1|d2|j.d3}|j.d4}t|}|t|k(sJ|jt||jd#j-||jd#j-d5|D|j0|dD]}|j.|j2}t5|tr|j|>t5|t"t6fr|jt|o|jd#j-t9t|d6j-|j;}||||fS#t$rd }YwxYw#t$r|} YwxYw#t$r|} YCwxYw#t$rd } YwxYw)7Nzalignment target name 'z.' is too long (must not exceed 254 characters)rz.alignment target name cannot be blank or emptyrrzchromStart after chromEnd (z > rrvrM.zalignment query name 'z-' is too long (must not exceed 255 charactersrrizscore (z) must be between 0 and 1000)rr)rr+-z thickStart (z) after thickEnd (zthickStart out of range for :z, thick:zthickEnd out of range for r,c3NK|]}dt|cxkxrdkncyw)rN)r!)rJcolors rrKz2AlignmentWriter._extract_fields..0s!+VeAU,Ac,A,A+Vs#%lz?Expecting color to consist of r,g,b values from 0 to 255. Got '' r c32K|]}t|ywrFrH)rJrs rrKz2AlignmentWriter._extract_fields..@sK9IK rc32K|]}t|ywrFr)rJrgs rrKz2AlignmentWriter._extract_fields..CsNJJNrrwzUnexpected value z for bedN in _extract_fieldsexpIds expScoresc32K|]}t|ywrFr)rJexpScores rrKz2AlignmentWriter._extract_fields..MsH(H Hr )ryrrrGrxrqueryr3rirHrrkrlitemRgbrstripr-allr!rrsumrNrO annotationsrzr rXr'maprB)rrryrowrfrgrhr rirjrkrlrcolorsstepsalignedrornrpr r expCountr?valuerests r_extract_fieldszAlignmentWriter._extract_fieldssyy  ## u: )%0^_  u:>MN N**40 ((/ j :8*C |STUV V !8??%%DrzTS ,TF2_` JJt  !8 #!19 $wug5Q%RSSE  JJu  !8$$T*i.C.CE.JJ JJv  !8 (&11  JJs: ' !8 $--j($&zl2DXJaP?+zH/D$6tfAj\8*T\]g\hhijristq=h&;x(?R$4TF!J) U T)(T), T;:T;> U  U  UUc|j}d}d}d}d} d} g} |jdur t} n t} d} t j d}d}d}t |} t|}|j|\}}}}|| k7r| |}|} |dz }d|d< ||k(r|j}| j}|| kDr|} | j}|j|| jd| jd|r2|j}||z }|D]}|j|||| | }||_|dur | | fSd}|dk(rt#|}| j%|n|j&kDr||_|dz }|D]Q}|dk\r|d xxdz cc<||d z|d<||dkDs,|d xxdz cc<|dxx|d z cc<||dkDr&S|r|D]}|j)| | dz } |j+||}| j|zd z#t$r|}d}YwxYw) zWrite alignments to the output file, and return the number of alignments. alignments - A list or iterator returning Alignment objects stream - Output file stream. rrNTz=IIIFrrrrr)r~r| _ZippedStreamrstructStructiternextr StopIterationrgetvaluerrtruncate addOffsetSizeoffset_Regionr3raddKeysFromRowpack)rrrrrr~ritemIxsectionStartIx sectionEndIx currentChromrrr formatterdoneregionrrfrrrblockStartOffsetrr5blockEndOffsetrrrs rrz AlignmentWriter.write_alignmentsYs ((    ==D "_FYF MM&) *%  * , +/*>*>y*I'uc4L(#/!-#(LqLG()Ju%%#);;= {{},&#'L( T" A" %+[[]N .1A AI'4 #11,%*( &2N 0 4<*W$$){ %5v&vzz!  aKF! /CJ&K1$K!&W!5CJCJ&K1$KJ#g,.JCJ&  /#0HK..y,GH! >>'5#6D LLu, -q! % s$ H11 II)rwNNTir) r]r^r_r`fmtmoderrrrrrrcrds@rrrrrsN; C D 8#tL\A'F<"|p1dW%rrrcPeZdZdZdZdZdZdZdZdZ dZ d Z d Z d Z dd Zy )AlignmentIteratorzAlignment iterator for bigBed files. The pairwise alignments stored in the bigBed file are loaded and returned incrementally. Additional alignment information is stored as attributes of each alignment. rsrtc tj|}|j}|j}||_|j}|j }|j }t|}|j|t|j} |D]o} | j} |j| |j| j} | j| \ } }}}}}}}|_| tj k(roJ|j#|||_|j|t'j|dz|jd\}||_|j*dkDrd|_nd|_|j|j.t1|j||_|j|j4t|j||_|j9||_y)NQrrTF)rfromfilerrrrrrreadrformatter_headerrrrunpackr~r _read_autosqlrzr _lengthr _compressedrrr{rr_iterate_index_data)rrrrrrrrrr0 zoomLevelrr5rrnItems startChromId startBase endChromIdendBase endFileOffset dataCounts r _read_headerzAlignmentIterator._read_headers!!&)$$ ,, "&& "44..y) f#I.?? ! :I#//K KK $;;y~~.D  & ! 9 99 99 :  --ff= N#}}Y_fkk!nE    # #a '#D $D  F//0*95::6B  F**+#I.33F; ((0 rc.|j|jz }|j}|j|_|j |j|j |}tj|}|j|||j|SrF) rrrrryrr=rr@_analyze_fields)rrr autoSqlSizerr5rzs rr@zAlignmentIterator._read_autosqls|//&2F2FF && ,,  F((){{;'"--d3  [*dii@rc.d}t|jD].}||j}|||k7std||d|d||kDrg|_t||D]}||j}||j }d|vr+d|vr'd} |j d\}} |j}nd} |d vrt} n0|d vrt} n%|d k(rt} n|d vrt} ntd |z| r| } | fd} |jj|| gy)N) rfrgrhr rirjrkrlrmrnrorpzExpected field name 'z '; found 'rr rTF)r!r"r#r$)r%r&r')r'r(r)r*zUnknown field type %scx|jdjd}|Dcgc] }|| c}Scc}w)Nr)rr-)r5item_convertervaluesrs r converterz4AlignmentIterator._analyze_fields..converter!s4![[-33C8F?EFeN51FFFs7)rangeryr rx_custom_fieldsr r-r0r!rr'rH Exceptionr3) rrrrnamesr8r r=r< make_array_rUrSs rrOz!AlignmentIterator._analyze_fieldssL  tyy! A!9>>DuQx >CAhM  ) )"$D (*5 @AJ**Jj SJ%6! * 0 0 5 A'--/ " ?? 00! w&! EE  7* DEE!*3AG    & & I'> ?5 @rc # Ktj|jdz}|j}|j} |j }|d}#t $r%|j|j|j|j}|jdkDrtj|}|rM|j|d|\}}} |jd|dz} ||| } || d}||| | dt!| f|rM |j"} | Yyt%| j D]\} }t'|t'|k(sn t)d | j | dz}n#t*$r| }YnwxYwwY/wxYww)NIIIrrFailed to find child node)r r!rrrchildrenrrrr=rrBzlib decompressr?r1rGparent enumerater RuntimeError IndexError)rrr0rnoder_r5rrgrhr8rrbr1childs rrCz AlignmentIterator._iterate_index's MM$..5"89 ~~yy #==8 {="  DOO,{{4==1##a'??40D4=4D4DT%4[4Q1GZ 1d+a/AQ|j| j|j| j} |jdkDrt!j"| } |j$dk(rJ|j'| d|\}}}||k(r||kr||ks||k(r||k(s||k(r|||| |t)| fnd}t)| }||kru||z}|j'| ||\}}}|}| j+d|dz}| ||}|}||k7rF||ks||kr||k7rV||k7r||k7ra||||dt)|f||kruYwxYw#t4$r|} YnwxYwíw)Nr]rTFrrr^)r r!rrrr_ endChromIxrJ startChromIxrHrrrr=rrBr`rar~r?rGr1rbrcrrdre)rrchromIxrrr0r padded_start padded_endrfr_ visit_childrgr5 child_chromIxchild_chromStartchild_chromEndr8nr9rrbr1s r _search_indexzAlignmentIterator._search_indexPs MM$..5"89 ~~qy 1W yy> ==f$ %E((%--8G\;RR ,0B0BEOO/TT "&K  D>$-foo$>DLE5$x2e9,D''BCC!??5195D]"0  DOO,{{4==1##a'??40D$$)FOFVFVUd GCM#3^%/,s2u~7M,>!1S!8E^A (/36>U;R (),* I !a%30 P""!D"sVAI& DBI&%I&4II&EI I&II& I!I& I!!I&c t|j}|\}}}}}}|j||||||S#t$rYywxYwrF)r#rDr$_create_alignment) rrrrrgrhr dataStartdataEnds r_read_next_alignmentz&AlignmentIterator._read_next_alignments_ tzz"CCF?XtY%% Z4G     s6 AAc||dz dk(sJ|||dz }|r |jjd}ng}|j|}|jdkDr|d} nd} |jdkDr|d} nd} |jdkDrdt |d } t j |d jd jd t} t j |d jd jd t} t| | k7rtd t| | fzt| | k7rtdt| | fzd}d}||gg}t| | D]<\}}||k7r|j||g|}||z }||z }|j||g>t j|t jj}t| }n1||z }t jd|gd|ggt j}|}|dddfxx|z cc<t!d|}t#|| }||g}| dk(r||dddfz |dddf<||dk7rtd||dfz||dk7rtd||dfzt%||}t||jdz kDrOi|_t||jdz d|j(D]\}}|\} }|||j&| <!|jdkr|S|d} t+|}|j-r t |} ||_|jd kr|St |d|_|jd kr|St |d|_|jd kr|S|d|_|S#t$rYwwxYw)Nrrrrvrrrrrrrrz:Inconsistent number of block sizes (%d found, expected %d)zDInconsistent number of block start positions (%d found, expected %d)lengthrrrz/Inconsistent chromStart found (%d, expected %d)rz-Inconsistent chromEnd found (%d, expected %d)r)r,r-r{ryr!rfromiterrrGrxzipr3rintp transposerrrrrrWr' is_integerrirkrlr)rrrgrhrrvrwwords target_recordr rjrnro blockStarts tPosition qPositionrr blockStartqSizequery_sequence query_recordrecordsrr7 custom_fieldrUris rruz#AlignmentIterator._create_alignmentsGaK A%%%I! , KKM''-EE W- 99q=8DD 99q=1XFF 99q=U1XJU1X__S%9%?%?%DcJJ++eAhooc&:&@&@&EsKK:*, P: 34;:- Z;'45II%y12K),Z)E ;% :*&& I'>? *IY& Y& ""Iy#9:  ;((;8BBDK OE :-I((Q NQ N#CRWWMKEAqDZ'T%0 D9  ,/ S= % AqD(9 9K1  T* *A{4012  {5) )?[/01 g{3 u: A %$&I !&)% A *@$BUBU&V >"l".i.7o %%d+ > 99> a #%LE!E   99> "58}  99>  q]  99> !!H    s& N99 OOc|jSrF)rArUs r__len__zAlignmentIterator.__len__s ||rNc #K|j}|||ktdt|jD]\}}|j|k(sntd|z||d}t |}ntd||dz}|j |||}|D]%}|\}} } } } } |j|| | | | | }|'yw)aIterate over alignments overlapping the specified chromosome region.. This method searches the index to find alignments to the specified chromosome that fully or partially overlap the chromosome region between start and end. Arguments: - chromosome - chromosome name. If None (default value), include all alignments. - start - starting position on the chromosome. If None (default value), use 0 as the starting position. - end - end position on the chromosome. If None (default value), use the length of the chromosome as the end position. Nz5start and end must both be None if chromosome is NonezFailed to find %s in alignmentsrz!end must be None if start is Noner)_streamrxrcr{rrGrsru)r chromosomerrrrkrr5rrgrhrrvrwrs rsearchzAlignmentIterator.searchs    CO K$-T\\#: Q99 * Q!!BZ!OPP};Ef+C$%HIIai!!&'5#> CFI CGZ4G..XtYIO  s AB? 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