o Rŀgn@sdZddlmZddlmZddlmZddlmZddlmZGdddeZGd d d eZGd d d eZ Gd ddeZ GdddeZ GdddeZ e dkr_ddlmZedSdS)zCommand line wrapper for bwa.) _Argument)_Option)_StaticArgument)_Switch)AbstractCommandlinec@eZdZdZdddZdS)BwaIndexCommandlineaCommand line wrapper for Burrows Wheeler Aligner (BWA) index. Index database sequences in the FASTA format, equivalent to:: $ bwa index [-p prefix] [-a algoType] [-c] See http://bio-bwa.sourceforge.net/bwa.shtml for details. Examples -------- >>> from Bio.Sequencing.Applications import BwaIndexCommandline >>> reference_genome = "/path/to/reference_genome.fasta" >>> index_cmd = BwaIndexCommandline(infile=reference_genome, algorithm="bwtsw") >>> print(index_cmd) bwa index -a bwtsw /path/to/reference_genome.fasta You would typically run the command using index_cmd() or via the Python subprocess module, as described in the Biopython tutorial. bwac Ksp||_tdtgdddddddtgd d ddd td gd dddtddgdg|_tj||fi|dS)Initialize the class.index)-aa algorithmaAlgorithm for constructing BWT index. Available options are: - is: IS linear-time algorithm for constructing suffix array. It requires 5.37N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB. IS is the default algorithm due to its simplicity. - bwtsw: Algorithm implemented in BWT-SW. This method works with the whole human genome, but it does not work with database smaller than 10MB and it is usually slower than IS.cSs|dvS)N)isbwtswxrrT/var/www/html/myenv/lib/python3.10/site-packages/Bio/Sequencing/Applications/_bwa.py7sz.BwaIndexCommandline.__init__..FT)checker_functionequate is_required)-ppprefixz3Prefix of the output database [same as db filename])rrinfilezInput file namefilenamer-cczGBuild color-space index. The input fasta should be in nucleotide space.N) program_namerrrr parametersr__init__selfcmdkwargsrrrr#&s, zBwaIndexCommandline.__init__Nr __name__ __module__ __qualname____doc__r#rrrrrsrc@r)BwaAlignCommandlinea8Command line wrapper for Burrows Wheeler Aligner (BWA) aln. Run a BWA alignment, equivalent to:: $ bwa aln [...] > See http://bio-bwa.sourceforge.net/bwa.shtml for details. Examples -------- >>> from Bio.Sequencing.Applications import BwaAlignCommandline >>> reference_genome = "/path/to/reference_genome.fasta" >>> read_file = "/path/to/read_1.fq" >>> output_sai_file = "/path/to/read_1.sai" >>> align_cmd = BwaAlignCommandline(reference=reference_genome, read_file=read_file) >>> print(align_cmd) bwa aln /path/to/reference_genome.fasta /path/to/read_1.fq You would typically run the command line using align_cmd(stdout=output_sai_file) or via the Python subprocess module, as described in the Biopython tutorial. r cKs||_tdtdgddddtdgddddtdd gd d d d dtddgd dd d dtddgddd d dtddgddd d dtddgddd d dtddgd d!d d dtd"d#gd$d%d d dtd&d'gd(d)d d dtd*d+gd,d-d d dtd.d/gd0d1d d dtd2d3gd4d5d d dtd6d7gd8d9d d dtd:d;gdd?gd@dAd d dtdBdCgdDtdEdFgdGtdHdIgdJtdKdLgdMtdNdOgdPtdQdRgdSg|_tj||fi|dTS)Ur aln referenceReference file nameTr read_filezRead file name-nnzMaximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]cSt|ttfSN isinstanceintfloatrrrrrnz.BwaAlignCommandline.__init__..Frr-oocSr5r6r7rrrrrtr;z-eezWMaximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]cS t|tSr6r8r9rrrrrz -ddz=Disallow a long deletion within INT bp towards the 3-end [16]cSr@r6rArrrrrrBz-iiz4Disallow an indel within INT bp towards the ends [5]cSr@r6rArrrrrrBz-llzTake the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for -k 2. [inf]cSr@r6rArrrrrrB-kkz%Maximum edit distance in the seed [2]cSr@r6rArrrrrrB-ttz,Number of threads (multi-threading mode) [1]cSr@r6rArrrrrrB-MMziMismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]cSr@r6rArrrrrrB-OOzGap open penalty [11]cSr@r6rArrrrrrB-EEzGap extension penalty [4]cSr@r6rArrrrrrB-RRa7Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).cSr@r6rArrrrrrB-qqzParameter for read trimming [0]. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l > See http://bio-bwa.sourceforge.net/bwa.shtml for details. Examples -------- >>> from Bio.Sequencing.Applications import BwaSamseCommandline >>> reference_genome = "/path/to/reference_genome.fasta" >>> read_file = "/path/to/read_1.fq" >>> sai_file = "/path/to/read_1.sai" >>> output_sam_file = "/path/to/read_1.sam" >>> samse_cmd = BwaSamseCommandline(reference=reference_genome, ... read_file=read_file, sai_file=sai_file) >>> print(samse_cmd) bwa samse /path/to/reference_genome.fasta /path/to/read_1.sai /path/to/read_1.fq You would typically run the command line using samse_cmd(stdout=output_sam_file) or via the Python subprocess module, as described in the Biopython tutorial. r c Ks||_tdtdgddddtdgddddtdgd dddtd d gd d dddtddgdddddg|_tj||fi|dS)r samser0r1Trsai_filez Sai file namer2zRead file namer3r4zMaximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]cSr@r6rArrrrrrBz.BwaSamseCommandline.__init__..Fr<-rrCSpecify the read group in a format like '@RG ID:foo SM:bar'. [null]cSr@r6rArrrrrrBNr!rrrr"rr#r$rrrr#s.  zBwaSamseCommandline.__init__Nr(r)rrrrr`sr`c@r)BwaSampeCommandlineaoCommand line wrapper for Burrows Wheeler Aligner (BWA) sampe. Generate alignments in the SAM format given paired-end reads. Equivalent to:: $ bwa sampe [...] > See http://bio-bwa.sourceforge.net/bwa.shtml for details. Examples -------- >>> from Bio.Sequencing.Applications import BwaSampeCommandline >>> reference_genome = "/path/to/reference_genome.fasta" >>> read_file1 = "/path/to/read_1.fq" >>> read_file2 = "/path/to/read_2.fq" >>> sai_file1 = "/path/to/read_1.sai" >>> sai_file2 = "/path/to/read_2.sai" >>> output_sam_file = "/path/to/output.sam" >>> read_group = r"@RG\tID:foo\tSM:bar" # BWA will turn backslash-t into tab >>> sampe_cmd = BwaSampeCommandline(reference=reference_genome, ... sai_file1=sai_file1, sai_file2=sai_file2, ... read_file1=read_file1, read_file2=read_file2, ... r=read_group) >>> print(sampe_cmd) bwa sampe /path/to/reference_genome.fasta /path/to/read_1.sai /path/to/read_2.sai /path/to/read_1.fq /path/to/read_2.fq -r @RG\tID:foo\tSM:bar You would typically run the command line using sampe_cmd(stdout=output_sam_file) or via the Python subprocess module, as described in the Biopython tutorial. r cKs||_tdtdgddddtdgddddtdgd dddtd gd dddtd gd dddtddgdddddtddgdddddtddgdddddtddgdd dddtd!d"gd#d$dddg |_tj||fi|d%S)&r samper0r1Tr sai_file1z Sai file 1 sai_file2z Sai file 2 read_file1z Read file 1 read_file2z Read file 2r r zMaximum insert size for a read pair to be considered being mapped properly [500]. Since 0.4.5, this option is only used when there are not enough good alignments to infer the distribution of insert sizes.cSr@r6rArrrrrRrBz.BwaSampeCommandline.__init__..Fr<r=r>zMaximum occurrences of a read for pairing [100000]. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing.cSr@r6rArrrrr[rBr3r4zMaximum number of alignments to output in the XA tag for reads paired properly [3]. If a read has more than INT hits, the XA tag will not be written.cSr@r6rArrrrrcrBrWrXzMaximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) [10]. If a read has more than INT hits, the XA tag will not be written.cSr@r6rArrrrrkrBrcrdrecSr@r6r8strrrrrrqrBNrfr$rrrr#@sR   2zBwaSampeCommandline.__init__Nr(r)rrrrrgs!rgc@r)BwaBwaswCommandlineaCommand line wrapper for Burrows Wheeler Aligner (BWA) bwasw. Align query sequences from FASTQ files. Equivalent to:: $ bwa bwasw [...] See http://bio-bwa.sourceforge.net/bwa.shtml for details. Examples -------- >>> from Bio.Sequencing.Applications import BwaBwaswCommandline >>> reference_genome = "/path/to/reference_genome.fasta" >>> read_file = "/path/to/read_1.fq" >>> bwasw_cmd = BwaBwaswCommandline(reference=reference_genome, read_file=read_file) >>> print(bwasw_cmd) bwa bwasw /path/to/reference_genome.fasta /path/to/read_1.fq You would typically run the command line using bwasw_cmd() or via the Python subprocess module, as described in the Biopython tutorial. r cKsL||_tdtdgddddtdgddddtdgd dd dtd d gd ddd dtddgdddd dtddgdddd dtddgdddd dtddgdd dd dtd!d"gd#d$dd dtd%d&gd'd(dd dtd)d*gd+d,dd dtd-d.gd/d0dd dtd1d2gd3d4dd dtd5d6gd7d8dd dg|_tj||fi|d9S):r bwaswr0r1Trr2z Read file mate_filez Mate fileFr r zScore of a match [1]cSr@r6rArrrrrrBz.BwaBwaswCommandline.__init__..r<rZr[zMismatch penalty [3]cSr@r6rArrrrrrBrSrTzGap open penalty [5]cSr@r6rArrrrrrBrcrdzOGap extension penalty. The penalty for a contiguous gap of size k is q+k*r. [2]cSr@r6rArrrrrrBrIrJz1Number of threads in the multi-threading mode [1]cSr@r6rArrrrrrB-wwz'Band width in the banded alignment [33]cSr@r6rArrrrrrB-TTz)Minimum score threshold divided by a [37]cSr@r6rArrrrrrBrr zCoefficient for threshold adjustment according to query length [5.5]. Given an l-long query, the threshold for a hit to be retained is a*max{T,c*log(l)}.cSr@r6)r8r:rrrrrrBz-zzzIZ-best heuristics. Higher -z increases accuracy at the cost of speed. [1]cSr@r6rArrrrrrBz-ssz{Maximum SA interval size for initiating a seed [3]. Higher -s increases accuracy at the cost of speed.cSr@r6rArrrrrrBrWrXzYMinimum number of seeds supporting the resultant alignment to skip reverse alignment. [5]cSr@r6rArrrrrrBNrfr$rrrr#s  OzBwaBwaswCommandline.__init__Nr(r)rrrrroxsroc@r)BwaMemCommandlinea_Command line wrapper for Burrows Wheeler Aligner (BWA) mem. Run a BWA-MEM alignment, with single- or paired-end reads, equivalent to:: $ bwa mem [...] > See http://bio-bwa.sourceforge.net/bwa.shtml for details. Examples -------- >>> from Bio.Sequencing.Applications import BwaMemCommandline >>> reference_genome = "/path/to/reference_genome.fasta" >>> read_file = "/path/to/read_1.fq" >>> output_sam_file = "/path/to/output.sam" >>> align_cmd = BwaMemCommandline(reference=reference_genome, read_file1=read_file) >>> print(align_cmd) bwa mem /path/to/reference_genome.fasta /path/to/read_1.fq You would typically run the command line using align_cmd(stdout=output_sam_file) or via the Python subprocess module, as described in the Biopython tutorial. r cKs||_tdtdgddddtdgddddtdgd dd dtd d gd ddd dtddgdddd dtddgdddd dtddgdddd dtddgdd dd dtd!d"gd#d$dd dtd%d&gd'd(dd dtd)d*gd+d,dd dtd-d.gd/d0dd dtd1d2gd3d4dd dtd5d6gd7d8dd dtd9d:gd;dgd?d@dd dtdAdBgdCdDdd dtdEdFgdGdHdd dtdIdJgdKtdLdMgdNtdOdPgdQtdRdSgdTtdUdVgdWtdXdYgdZg|_tj||fi|d[S)\r memr0r1TrrkzRead 1 file namerlzRead 2 file nameFrIrJzNumber of threads [1]cSr@r6rArrrrr rBz,BwaMemCommandline.__init__..r<rGrHzMinimum seed length. Matches shorter than INT will be missed. The alignment speed is usually insensitive to this value unless it significantly deviates 20. [19]cSr@r6rArrrrrrBrrrszBand width. Essentially, gaps longer than INT will not be found. Note that the maximum gap length is also affected by the scoring matrix and the hit length, not solely determined by this option. [100]cSr@r6rArrrrrrBrCrDaOff-diagonal X-dropoff (Z-dropoff). Stop extension when the difference between the best and the current extension score is above \|i-j\|*A+INT, where i and j are the current positions of the query and reference, respectively, and A is the matching score. Z-dropoff is similar to BLAST's X-dropoff except that it doesn't penalize gaps in one of the sequences in the alignment. Z-dropoff not only avoids unnecessary extension, but also reduces poor alignments inside a long good alignment. [100]cSr@r6rArrrrrrBrcrdzTrigger re-seeding for a MEM longer than minSeedLen*FLOAT. This is a key heuristic parameter for tuning the performance. Larger value yields fewer seeds, which leads to faster alignment speed but lower accuracy. [1.5]cSr5r6r7rrrrr%r;rr ziDiscard a MEM if it has more than INT occurrence in the genome. This is an insensitive parameter. [10000]cSr@r6rArrrrr+rBz-AAzMatching score. [1]cSr@r6rArrrrr1rBrUrVz[Mismatch penalty. The sequence error rate is approximately: {.75 * exp[-log(4) * B/A]}. [4]cSr@r6rArrrrr7rBrMrNzGap open penalty. [6]cSr@r6rArrrrr=rBrOrPzfGap extension penalty. A gap of length k costs O + k*E (i.e. -O is for opening a zero-length gap). [1]cSr@r6rArrrrrCrBz-LLaAClipping penalty. When performing SW extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best SW score minus the clipping penalty, clipping will not be applied. Note that in this case, the SAM AS tag reports the best SW score; clipping penalty is not deducted. [5]cSr@r6rArrrrrIrBz-UUzPenalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as scoreRead1+scoreRead2-INT and scores a paired as scoreRead1+scoreRead2-insertPenalty. It compares these two scores to determine whether we should force pairing. [9] cSr@r6rArrrrrOrBrQrRzComplete read group header line. 't' can be used in STR and will be converted to a TAB in the output SAM. The read group ID will be attached to every read in the output. An example is '@RG ID:foo SM:bar'. [null]cSr@r6rmrrrrrUrBrtruzWDon't output alignment with score lower than INT. This option only affects output. [30]cSr@r6rArrrrr[rBz-vvaFControl the verbose level of the output. This option has not been fully supported throughout BWA. Ideally, a value 0 for disabling all the output to stderr; 1 for outputting errors only; 2 for warnings and errors; 3 for all normal messages; 4 or higher for debugging. When this option takes value 4, the output is not SAM. [3]cSr@r6rArrrrrarBz-PPzrIn the paired-end mode, perform SW to rescue missing hits only but do not try to find hits that fit a proper pair.rrzmAssume the first input query file is interleaved paired-end FASTA/Q. See the command description for details.r r zOutput all found alignments for single-end or unpaired paired-end reads. These alignments will be flagged as secondary alignments.z-CCa-Append FASTA/Q comment to SAM output. This option can be used to transfer read meta information (e.g. barcode) to the SAM output. Note that the FASTA/Q comment (the string after a space in the header line) must conform the SAM spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output.z-HHzUse hard clipping 'H' in the SAM output. This option may dramatically reduce the redundancy of output when mapping long contig or BAC sequences.rKrLz@Mark shorter split hits as secondary (for Picard compatibility).Nr^r$rrrr#s   ~zBwaMemCommandline.__init__Nr(r)rrrrrxr_rx__main__) run_doctestN)r-Bio.Applicationrrrrrrr.r`rgrorxr* Bio._utilsrrrrrs$     :9Zl