DUfFdZddlZddlZddlZd dZdZd dZdZd dZdS) z4 Module to help create scaled bigWig files from BAM NFc|dz}tj|rN|sLt|D]<}|drt |}|cSddddd|g}tj|tj tj }| \}}|j rtd |zt |}tj|sIt|d } | t|d z| |S) z| Scale is cached in a bam.scale file containing the number of mapped reads. Use force=True to override caching. z.scale#samtoolsviewz-cz-F0x4stdoutstderrzsamtools says: %sw )ospathexistsopen startswithfloatstrip subprocessPopenPIPE communicate returncode ValueErrorwritestrclose) bamforcescale_fnline readcountcmdspr r fouts V/var/www/html/software/conda/lib/python3.11/site-packages/pybedtools/contrib/bigwig.pymapped_read_countr& s5 X~H w~~hNN  Ds## djjll++I    dE3 7DjojoNNNA]]__NFF|7,v5666f I 7>>( # #Hc"" 3y>>D())) ctjtj|}d|j||g} t j|tjtj}|\}}n#t$rtdwxYw|j r+tdd |d|d||S)NbedGraphToBigWigrbedGraphToBigWig was not found on the path. This is an external tool from UCSC which can be downloaded from http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use `conda install ucsc-bedgraphtobigwig`cmds:   stderr: stdout: pybedtoolschromsizes_to_file chromsizesfnrrrrFileNotFoundErrorrrjoin)bedgraphgenomeoutput genome_filer"r#r r s r%bedgraph_to_bigwigr:'s/ 0Ef0M0MNNK  [& AD   T*/*/ R R R     4     | j03 O    M AA66Bcd|g}||d|g||d|g||d|g||d|gtj}|| t j|t jt j}|\}} n#t$rtdwxYw|j r+tdd |d | d |tj|S) NbigWigToBedGraphz-chromz-startz-endz-udcDirrbigWigToBedGraph was not found on the path. This is an external tool from UCSC which can be downloaded from http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use `conda install ucsc-bedgraphtobigwig`r+r,r-r.) extendr0BedTool_tmpappendrrrrr4rrr5) r3chromstartendudcDirr"outfnr#r r s r%bigwig_to_bedgraphrH<sZ  #D  Xu%&&&  Xu%&&&  VSM"""  Y'(((   # # % %EKK   T*/*/ R R R     4     | j03 O     e $ $$s AC C:ctjtj|}d|j||g} t j|tjtj}|\}}n#t$rtdwxYw|j r+tdd |d|d||S)N wigToBigWigrr>r+r,r-r.r/)wigr7r8r9r"r#r r s r% wig_to_bigwigrL[s/ 0Ef0M0MNNK 36; 7D   T*/*/ R R R     4     | j03 O    Mr;cbtjtj|}tdd|}|rt |}d|dz z }||d<tj|jdi|}d|j||g} tj | tj tj d} | \} } n#t$rtdwxYw| j rd | vrtd |} | j| d< tj | tj tj d} | \} } n#t$rtd wxYw| j r+t!d d | d| d| dS)a Given a BAM file `bam` and assembly `genome`, create a bigWig file scaled such that the values represent scaled reads -- that is, reads per million mapped reads. (Disable this scaling step with scale=False; in this case values will indicate number of reads) Assumes that `bedGraphToBigWig` from UCSC tools is installed; see http://genome.ucsc.edu/goldenPath/help/bigWig.html for more details on the format. T)bgsplitgg.Ascaler))r r universal_newlinesr*bedSortz+BAM header was not sorted; sorting bedGraphzbedSort was not found on the path. This is an external tool from UCSC which can be downloaded from http://hgdownload.soe.ucsc.edu/admin/exe/. Alternatatively, use `conda install ucsc-bedgraphtobigwig`r+r,z stderr: z stdout: N)r0r1r2dictr&r@genome_coverager3rrrrr4rprintsortrr5)rr7r8rRr9kwargsr!_scalexr"r#r r ys r% bam_to_bigwigr^ps/ 0Ef0M0MNNK T 5 5 5F !%c** i#o& w/ 3/99&99A k6 :D   ??#          4     | V++ ;<<< FFHH$Q  !!#' A ]]__NFFF    #8   | j25((4....&&&&& Q     sACC AE E:)F)NNNN) __doc__r0r rr&r:rHrLr^rUr'r%r`s <*%%%%>*< < < < < < r'