o Rŀg@s^dZddlmZddlmZddlmZddlmZddlmZddlmZGdd d eZGd d d eZ Gd d d eZ GdddeZ GdddeZ GdddeZ GdddeZGdddeZGdddeZGdddeZGdddeZGdddeZGd d!d!eZGd"d#d#eZGd$d%d%eZed&krdd'lmZed(Sd(S))z"Command line wrapper for samtools.) _Argument) _ArgumentList)_Option)_StaticArgument)_Switch)AbstractCommandlinec@eZdZdZdddZdS)SamtoolsViewCommandlineaCommand line wrapper for samtools view. Extract/print all or sub alignments in SAM or BAM format, equivalent to:: $ samtools view [-bchuHS] [-t in.refList] [-o output] [-f reqFlag] [-F skipFlag] [-q minMapQ] [-l library] [-r readGroup] [-R rgFile] | [region1 [...]] See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsViewCommandline >>> input_file = "/path/to/sam_or_bam_file" >>> samtools_view_cmd = SamtoolsViewCommandline(input_file=input_file) >>> print(samtools_view_cmd) samtools view /path/to/sam_or_bam_file samtoolscKsT||_tdtddgdtddgdtdd gd td d gd tddgdtddgdtddgddddddtddgddddddtd d!gd"dd#dd$td%d&gd'dd(dd$td)d*gd+dd,dd$td-d.gd/dd0dd$td1d2gd3ddd4ddtd5d6gd7dd8dd$td9d:gd;tdddd?td@gdAddBg|_tj||fi|dCS)DInitialize the class.view-bbzOutput in the BAM formatz-cczInstead of printing the alignments, only count them and print the total number. All filter options, such as '-f', '-F' and '-q', are taken into account-hhz Include the header in the output-uuzOutput uncompressed BAM. This option saves time spent on compression/decompression and is thus preferred when the output is piped to another samtools commandz-HHzOutput the header only-SSzuInput is in SAM. If @SQ header lines are absent, the '-t' option is required.z-tta This file is TAB-delimited. Each line must contain the reference name and the length of the reference, one line for each distinct reference; additional fields are ignored. This file also defines the order of the reference sequences in sorting. If you run 'samtools faidx ', the resultant index file .fai can be used as this file.TFcS t|tSN isinstancestrxrY/var/www/html/myenv/lib/python3.10/site-packages/Bio/Sequencing/Applications/_samtools.pyU z2SamtoolsViewCommandline.__init__..filenameequatechecker_function-oo Output filecSrrrrrrr r!\r"-ffzYOnly output alignments with all bits in INT present in the FLAG fieldcSrrrintrrrr r!cr"r%r&-FFz(Skip alignments with bits present in INTcSrrr,rrrr r!ir"-qqz*Skip alignments with MAPQ smaller than INTcSrrr,rrrr r!or"-rrz#Only output reads in read group STRcSrrrrrrr r!ur"-RRz*Output reads in read groups listed in FILEcSrrrrrrr r!|r"-llz Only output reads in library STRcSrrrrrrr r!r"-1fast_bamz3Use zlib compression level 1 to compress the outputinput input_filezInput File Namer$ is_requiredregionRegion)r>N program_namerrrr parametersr__init__selfcmdkwargsrrr rD)s    dz SamtoolsViewCommandline.__init__Nr __name__ __module__ __qualname____doc__rDrrrr r r c@r)SamtoolsMpileupCommandlineaCommand line wrapper for samtools mpileup. Generate BCF or pileup for one or multiple BAM files, equivalent to:: $ samtools mpileup [-EBug] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-M capMapQ] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]] See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsMpileupCommandline >>> input = ["/path/to/sam_or_bam_file"] >>> samtools_mpileup_cmd = SamtoolsMpileupCommandline(input_file=input) >>> print(samtools_mpileup_cmd) samtools mpileup /path/to/sam_or_bam_file r cKs||_tdtddgdtddgdtdd gd td d gd tddgdddddtddgdddddtddgddddddtdd gd!ddd"ddtd#d$gd%dd&ddtd'd(gd)dd*ddtd+d,gd-dd.ddtd/d0gd1td2d3gd4td5d6gd7ddd8ddtd9d:gd;ddgd?td@dAgdBtdCdDgdEddFddtdGdHgdIddJddtdKdLgdMtdNdOgdPddQddtdRdSgdTddUddtdVdWgdXddYddtdZgd[ddd\g|_tj||fi|d]S)^r mpileup-EEzExtended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt specificity a little bitz-BBaPDisable probabilistic realignment for the computation of base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignmentsz-ggz`Compute genotype likelihoods and output them in the binary call format (BCF)rrzkSimilar to -g except that the output is uncompressed BCF, which is preferred for piping-CCaCoefficient for downgrading mapping quality for reads containing excessive mismatches. Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50FcSrrr,rrrr r!r"z5SamtoolsMpileupCommandline.__init__..r.r3r4z"Only generate pileup in region STRcSrrrrrrr r!r"r*r+zyThe faidx-indexed reference file in the FASTA format. The file can be optionally compressed by razipTcSrrrrrrr r!r"r#r7r8z{BED or position list file containing a list of regions or sites where pileup or BCF should be generatedcSrrrrrrr r!r"z-MMzCap Mapping Quality at McSrrr,rrrr r!r"r1r2z3Minimum mapping quality for an alignment to be usedcSrrr,rrrr r!r"-QQz0Minimum base quality for a base to be consideredcSrrr,rrrr r!r"z-6 illumina_13z3Assume the quality is in the Illumina 1.3+ encoding-AAz4Do not skip anomalous read pairs in variant calling.r rz*List of input BAM files, one file per linecSrrrrrrr r! r"z-ddz5At a position, read maximally INT reads per input BAMcSrrr,rrrr r!r"z-DDzOutput per-sample read depthrrzROutput per-sample Phred-scaled strand bias P-value-eezqPhred-scaled gap extension sequencing error probability. Reducing INT leads to longer indelscSrrr,rrrr r!r"rrzCoefficient for modeling homopolymer errors. Given an l-long homopolymer run, the sequencing error of an indel of size s is modeled as INT*s/lcSrrr,rrrr r!&r"-IIzDo not perform INDEL callingz-LLzSSkip INDEL calling if the average per-sample depth is above INTcSrrr,rrrr r!.r"r'r(zpPhred-scaled gap open sequencing error probability. Reducing INT leads to more indel calls.cSrrr,rrrr r!6r"z-ppa.Comma delimited list of platforms (determined by @RG-PL) from which indel candidates are obtained. It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINAcSrrrrrrr r!Ar"r<z!Input File for generating mpileupr=N)rBrrrrrCrrDrErrr rDs       z#SamtoolsMpileupCommandline.__init__NrIrJrrrr rPrOrPc@r)SamtoolsReheaderCommandlineaCommand line wrapper for samtools reheader. Replace the header in in.bam with the header in in.header.sam, equivalent to:: $ samtools reheader See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsReheaderCommandline >>> input_header = "/path/to/header_sam_file" >>> input_bam = "/path/to/input_bam_file" >>> reheader_cmd = SamtoolsReheaderCommandline(input_header=input_header, ... input_bam=input_bam) >>> print(reheader_cmd) samtools reheader /path/to/header_sam_file /path/to/input_bam_file r cKN||_tdtgdddddtgdddddg|_tj||fi|dS) r reheader) input_header header_samsam_filezSam file with headerTr=) input_bamr<bam_filezBAM file for writing header toNrBrrrCrrDrErrr rDc z$SamtoolsReheaderCommandline.__init__NrIrJrrrr rfMrfc@r)SamtoolsCatCommandlineatCommand line wrapper for samtools cat. Concatenate BAMs, equivalent to:: $ samtools cat [-h header.sam] [-o out.bam] [ ... ] See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsCatCommandline >>> input_bam1 = "/path/to/input_bam1" >>> input_bam2 = "/path/to/input_bam2" >>> input_bams = [input_bam1, input_bam2] >>> samtools_cat_cmd = SamtoolsCatCommandline(input_bam=input_bams) >>> print(samtools_cat_cmd) samtools cat /path/to/input_bam1 /path/to/input_bam2 r c Ksl||_tdtddgdddddd td d gd ddd dd tgdddddg|_tj||fi|dS)r catrrzHeader SAM fileTFcSrrrrrrr r!r"z1SamtoolsCatCommandline.__init__..r#r'r(zOutput SAM filecSrrrrrrr r!r")r;rlbamszInput BAM filesr=N)rBrrrrCrrDrErrr rDs0zSamtoolsCatCommandline.__init__NrIrJrrrr rqxrOrqc@r) SamtoolsVersion0xSortCommandlineagCommand line wrapper for samtools version 0.1.x sort. Concatenate BAMs, equivalent to:: $ samtools sort [-no] [-m maxMem] See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsVersion0xSortCommandline >>> input_bam = "/path/to/input_bam" >>> out_prefix = "/path/to/out_prefix" >>> samtools_sort_cmd = SamtoolsVersion0xSortCommandline(input=input_bam, out_prefix=out_prefix) >>> print(samtools_sort_cmd) samtools sort /path/to/input_bam /path/to/out_prefix r c Ksx||_tdtddgdtddgdtdd gd d d d dtdgddddtdgddddg|_tj||fi|dS)r sortr'r(zUOutput the final alignment to the standard output-nn]Sort by read names rather than by chromosomal coordinates-mm)Approximately the maximum required memoryFcSrrr,rrrr r!r"z;SamtoolsVersion0xSortCommandline.__init__..r.r;zInput BAM fileTr= out_prefixz Output prefixNrArErrr rDs(z)SamtoolsVersion0xSortCommandline.__init__NrIrJrrrr rtrtc@r) SamtoolsVersion1xSortCommandlineaCommand line wrapper for samtools version 1.3.x sort. Concatenate BAMs, equivalent to:: $ samtools sort [-n] [-T FREFIX] [-o file] [-I INT] [-m maxMem] See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsVersion1xSortCommandline >>> input_bam = "/path/to/input_bam" >>> FREFIX = "/path/to/out_prefix" >>> file_name = "/path/to/out_file" >>> samtools_sort_cmd = SamtoolsVersion1xSortCommandline(input=input_bam, T=FREFIX, o=file_name) >>> print(samtools_sort_cmd) samtools sort -o /path/to/out_file -T /path/to/out_prefix /path/to/input_bam r c Ks||_tdtddgdtddgddd d d td d gdddd d tddgdddd d tddgdddd d tddgdddd d tdgddddg|_tj||fi|d S)!r rurvrwrxr'r(z`(file) Write the final sorted output to FILE, rather than to standard outputFcSrrrrrrr r!r"z;SamtoolsVersion1xSortCommandline.__init__..r.z-OOz4(FORMAT) Write the final output as sam, bam, or cramcSrrrrrrr r!r"z-TTz(PREFIX) Write temporary files to PREFIX.nnnn.bam, or if the specified PREFIX is an existing directory, to PREFIX/samtools.mmm.mmm.tmp.nnnn.bam, where mmm is unique to this invocation of the sort commandcSrrrrrrr r!r"rbrca(INT) Set the desired compression level for the final output file, ranging from 0 (uncompressed) or 1 (fastest but minimal compression) to 9 (best compression but slowest to write), similarly to gzip(1)'s compression level setting.cSrrrrrrr r!r"ryrzr{cSrrr,rrrr r!r"r;zInput SAM/BAM/CRAM fileTr=NrArErrr rDsR .z)SamtoolsVersion1xSortCommandline.__init__NrIrJrrrr r~rOr~c@r)SamtoolsMergeCommandlineaCommand line wrapper for samtools merge. Merge multiple sorted alignments, equivalent to:: $ samtools merge [-nur1f] [-h inh.sam] [-R reg] [...] See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsMergeCommandline >>> out_bam = "/path/to/out_bam" >>> in_bam = ["/path/to/input_bam1", "/path/to/input_bam2"] >>> merge_cmd = SamtoolsMergeCommandline(out_bam=out_bam, ... input_bam=in_bam) >>> print(merge_cmd) samtools merge /path/to/out_bam /path/to/input_bam1 /path/to/input_bam2 r cKs||_tdtddgdtddgdtdd gd td d gd tddgdtddgddddddtddgdddddtgddddd tgd!d"ddd g |_tj||fi|d#S)$r mergervrwzhThe input alignments are sorted by read names rather than by chromosomal coordinatesr3r4zaAttach an RG tag to each alignment. The tag value is inferred from file namesrrzUncompressed BAM outputr9r:z^Use zlib compression level 1 to compress the outputr*r+zQForce to overwrite the output file if presentrrz`Use the lines of FILE as '@' headers to be copied to out.bamTFcSrrrrrrr r!\r"z3SamtoolsMergeCommandline.__init__..r#r5r6z4Merge files in the specified region indicated by STRcSrrrrrrr r!br"r.) output_bamout_bamoutoutputzOutput BAM filer=)rlin_bamr;bam Input BAMN) rBrrrrrrCrrDrErrr rD<s\ 2z!SamtoolsMergeCommandline.__init__NrIrJrrrr r&rprc@r)SamtoolsIndexCommandlineaCommand line wrapper for samtools index. Index sorted alignment for fast random access, equivalent to:: $ samtools index See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsIndexCommandline >>> input = "/path/to/aln_bam" >>> samtools_index_cmd = SamtoolsIndexCommandline(input_bam=input) >>> print(samtools_index_cmd) samtools index /path/to/aln_bam r cK6||_tdtgddg|_tj||fi|dS)r indexr;rrlBAM file to be indexedNrnrErrr rD  z!SamtoolsIndexCommandline.__init__NrIrJrrrr rtrc@r)SamtoolsIdxstatsCommandlineaCommand line wrapper for samtools idxstats. Retrieve and print stats in the index file, equivalent to:: $ samtools idxstats See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsIdxstatsCommandline >>> input = "/path/to/aln_bam" >>> samtools_idxstats_cmd = SamtoolsIdxstatsCommandline(input_bam=input) >>> print(samtools_idxstats_cmd) samtools idxstats /path/to/aln_bam r cKr)r idxstatsrrNrnrErrr rDrz$SamtoolsIdxstatsCommandline.__init__NrIrJrrrr rrrc@r)SamtoolsFaidxCommandlineaCommand line wrapper for samtools faidx. Retrieve and print stats in the index file, equivalent to:: $ samtools faidx [region1 [...]] See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsFaidxCommandline >>> reference = "/path/to/reference.fasta" >>> samtools_faidx_cmd = SamtoolsFaidxCommandline(reference=reference) >>> print(samtools_faidx_cmd) samtools faidx /path/to/reference.fasta r cKs<||_tdtgdddddg|_tj||fi|dS)r faidx referencereference_fastarefReference FASTA to be indexedTr=NrnrErrr rDs z!SamtoolsFaidxCommandline.__init__NrIrJrrrr rrrc@r)SamtoolsFixmateCommandlineaCommand line wrapper for samtools fixmate. Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment, equivalent to:: $ samtools fixmate See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsFixmateCommandline >>> in_bam = "/path/to/in.nameSrt.bam" >>> out_bam = "/path/to/out.bam" >>> fixmate_cmd = SamtoolsFixmateCommandline(input_bam=in_bam, ... out_bam=out_bam) >>> print(fixmate_cmd) samtools fixmate /path/to/in.nameSrt.bam /path/to/out.bam r cKrg) r fixmater sorted_bamrlr;r<Name Sorted Alignment File Tr=rrr output_filer)NrnrErrr rDroz#SamtoolsFixmateCommandline.__init__NrIrJrrrr rrprc@r)SamtoolsRmdupCommandlinea{Command line wrapper for samtools rmdup. Remove potential PCR duplicates, equivalent to:: $ samtools rmdup [-sS] See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsRmdupCommandline >>> input_sorted_bam = "/path/to/input.srt.bam" >>> out_bam = "/path/to/out.bam" >>> rmdup_cmd = SamtoolsRmdupCommandline(input_bam=input_sorted_bam, ... out_bam=out_bam) >>> print(rmdup_cmd) samtools rmdup /path/to/input.srt.bam /path/to/out.bam r c Ksf||_tdtddgdtddgdtgdd d d d tgd d d d d g|_tj||fi|dS)r rmdupz-sszRemove duplicates for single-end reads. By default, the command works for paired-end reads onlyrrzNTreat paired-end reads as single-end readsrrTr=rr)N)rBrrrrCrrDrErrr rDs0z!SamtoolsRmdupCommandline.__init__NrIrJrrrr rrOrc@r)SamtoolsCalmdCommandlineaCommand line wrapper for samtools calmd. Generate the MD tag, equivalent to:: $ samtools calmd [-EeubSr] [-C capQcoef] See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsCalmdCommandline >>> input_bam = "/path/to/aln.bam" >>> reference_fasta = "/path/to/reference.fasta" >>> calmd_cmd = SamtoolsCalmdCommandline(input_bam=input_bam, ... reference=reference_fasta) >>> print(calmd_cmd) samtools calmd /path/to/aln.bam /path/to/reference.fasta r cKs||_tdtddgdtddgdtdd gd td d gd tddgdtddgdtddgdtddgdddddtgddd d d!tgd"d#d d d!g |_tj||fi|d$S)%r calmdrRrSzExtended BAQ calculation. This option trades specificity for sensitivity, though the effect is minor.r`razConvert the read base to = if it is identical to the aligned reference base. Indel caller does not support the = bases at the moment.rrzOutput uncompressed BAMr rzOutput compressed BAM rrz#The input is SAM with header lines r3r4zYCompute the BQ tag (without -A) or cap base quality by BAQ (with -A).r\r]z^When used jointly with -r this option overwrites the original base qualityrVrWzCoefficient to cap mapping quality of poorly mapped reads. See the pileup command for details.FcSrrr,rrrr r!mr"z3SamtoolsCalmdCommandline.__init__..r.)r;r<rinfilerlrTr=rrNrArErrr rDFsR    3z!SamtoolsCalmdCommandline.__init__NrIrJrrrr r1rOrc@r)SamtoolsTargetcutCommandlineaCommand line wrapper for samtools targetcut. This command identifies target regions by examining the continuity of read depth, computes haploid consensus sequences of targets and outputs a SAM with each sequence corresponding to a target, equivalent to:: $ samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2 em2] [-f ref] See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsTargetcutCommandline >>> input_bam = "/path/to/aln.bam" >>> samtools_targetcut_cmd = SamtoolsTargetcutCommandline(input_bam=input_bam) >>> print(samtools_targetcut_cmd) samtools targetcut /path/to/aln.bam r c Ks||_tdtddgdddddtd d gd dd ddtd dgddddddtddgdddddtddgdddddtddgdddddtgdddddg|_tj||fi|dS) r targetcutrYrZzMinimum Base Quality FcSrrr,rrrr r!r"z7SamtoolsTargetcutCommandline.__init__..r.z-iizInsertion PenaltycSrrr,rrrr r!r"r*r+zReference FilenameTcSrrrrrrr r!r"r#z-0em0cSrrrrrrr r!r"r9em1cSrrrrrrr r!r"z-2em2cSrrrrrrr r!r"r;rlr Input filer=N)rBrrrrCrrDrErrr rDs^.z%SamtoolsTargetcutCommandline.__init__NrIrJrrrr rsrc@r)SamtoolsPhaseCommandlinea9Command line wrapper for samtools phase. Call and phase heterozygous SNPs, equivalent to:: $ samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] See http://samtools.sourceforge.net/samtools.shtml for more details Examples -------- >>> from Bio.Sequencing.Applications import SamtoolsPhaseCommandline >>> input_bam = "/path/to/in.bam" >>> samtools_phase_cmd = SamtoolsPhaseCommandline(input_bam=input_bam) >>> print(samtools_phase_cmd) samtools phase /path/to/in.bam r c Ks||_tdtgdddddtddgdtd d gd dd d ddtddgdtddgdd dddtddgdd dddtddgdd dddg|_tj||fi|d S)!r phaserrTr=r\r]zDrop reads with ambiguous phaser rzPrefix of BAM outputFcSrrrrrrr r!r"z3SamtoolsPhaseCommandline.__init__..r#r/r0z$Do not attempt to fix chimeric readsz-kkz Maximum length for local phasingcSrrr,rrrr r!r"r.r1r2zCMinimum Phred-scaled LOD to call a heterozygotecSrrr,rrrr r!r"rYrZzBMinimum base quality to be used in het callingcSrrr,rrrr r!r"N)rBrrrrrCrrDrErrr rDsJ  &z!SamtoolsPhaseCommandline.__init__NrIrJrrrr rr}r__main__) run_doctestN)rNBio.Applicationrrrrrrr rPrfrqrtr~rrrrrrrrrrK Bio._utilsrrrrr s6      ;+21KN"+6NK@