def __init__(self, cmd="samtools", **kwargs): self.program_name = cmd self.parameters = [ _StaticArgument("merge"), _Switch(["-n", "n"], """The input alignments are sorted by read names rather than by chromosomal coordinates"""), _Switch(["-r", "r"], """Attach an RG tag to each alignment. The tag value is inferred from file names"""), _Switch(["-u", "u"], "Uncompressed BAM output"), _Switch(["-1", "fast_bam"], """Use zlib compression level 1 to compress the output"""), _Switch(["-f", "f"], """Force to overwrite the output file if present"""), _Option(["-h", "h"], """Use the lines of FILE as '@' headers to be copied to out.bam""", filename=True, equate=False, checker_function=lambda x: isinstance(x, str)), _Option(["-R", "R"], "Merge files in the specified region indicated by STR", equate=False, checker_function=lambda x: isinstance(x, str)), _Argument(["output_bam", "out_bam", "out", "output"], "Output BAM file", filename=True, is_required=True), _ArgumentList(["input_bam", "in_bam", "input", "bam"], "Input BAM", filename=True, is_required=True), ] AbstractCommandline.__init__(self, cmd, **kwargs)
def __init__(self, cmd="samtools", **kwargs): """Initialize the class.""" self.program_name = cmd self.parameters = [ _StaticArgument("cat"), _Option( ["-h", "h"], "Header SAM file", filename=True, equate=False, checker_function=lambda x: isinstance(x, str), ), _Option( ["-o", "o"], "Output SAM file", filename=True, equate=False, checker_function=lambda x: isinstance(x, str), ), _ArgumentList( ["input", "input_bam", "bams"], "Input BAM files", filename=True, is_required=True, ), ] AbstractCommandline.__init__(self, cmd, **kwargs)
def __init__(self, cmd="samtools", **kwargs): self.program_name = cmd self.parameters = [ _StaticArgument("cat"), _Option(["-h", "h"], "Header SAM file", filename=True, equate=False, checker_function=lambda x: isinstance(x, str)), _Option(["-o", "o"], "Output SAM file", filename=True, equate=False, checker_function=lambda x: isinstance(x, str)), _ArgumentList(["input", "input_bam", "bams"], "Input BAM files", filename=True, is_required=True) ] AbstractCommandline.__init__(self, cmd, **kwargs)
def __init__(self, cmd="gt", **kwargs): """ Construct and evaluate genometools merge commands. Example >>> x = Merge(infiles=["test.gff3"], tidy=True) >>> print(x) gt merge -tidy test.gff3 """ self.program_name = f"{cmd} merge" self.parameters = [ _StaticArgument("merge"), _Switch(["-tidy", "tidy"], ("Try to tidy the GFF3 files up during parsing.")), _Switch(["-retainids", "retainids"], ("when available, use the original IDs provided in the " "source file")), _Option( ["-o", "outfile"], "redirect output to specified file", checker_function=check_is_str, filename=True, equate=False, ), _Switch(["-gzip", "gzip"], "write gzip compressed output file."), _Switch( ["-bzip2", "bzip2"], "write bzip2 compressed output file.", ), _Switch( ["-force", "force"], "force writing to output file", ), _Switch(["-help", "help"], "Show help and exit"), _Switch(["-version", "version"], "display version information and exit"), _ArgumentList(["infiles"], "The GFF3 files to operate on.", checker_function=check_is_list_of_str, filename=True, is_required=True) ] super().__init__(cmd, **kwargs) return
def __init__(self, cmd="samtools", **kwargs): self.program_name = cmd self.parameters = [ _StaticArgument("mpileup"), _Switch(["-E", "E"], """Extended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt specificity a little bit"""), _Switch(["-B", "B"], """Disable 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 misalignments"""), _Switch(["-g", "g"], """Compute genotype likelihoods and output them in the binary call format (BCF)"""), _Switch(["-u", "u"], """Similar to -g except that the output is uncompressed BCF, which is preferred for piping"""), _Option(["-C", "C"], """Coefficient 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 50""", equate=False, checker_function=lambda x: isinstance(x, int)), _Option(["-r", "r"], "Only generate pileup in region STR", equate=False, checker_function=lambda x: isinstance(x, str)), _Option(["-f", "f"], """The faidx-indexed reference file in the FASTA format. The file can be optionally compressed by razip""", filename=True, equate=False, checker_function=lambda x: isinstance(x, str)), _Option(["-l", "l"], """BED or position list file containing a list of regions or sites where pileup or BCF should be generated""", filename=True, equate=False, checker_function=lambda x: isinstance(x, str)), _Option(["-M", "M"], "Cap Mapping Quality at M", equate=False, checker_function=lambda x: isinstance(x, int)), _Option(["-q", "q"], "Minimum mapping quality for an alignment to be used", equate=False, checker_function=lambda x: isinstance(x, int)), _Option(["-Q", "Q"], "Minimum base quality for a base to be considered", equate=False, checker_function=lambda x: isinstance(x, int)), _Switch(["-6", "illumina_13"], "Assume the quality is in the Illumina 1.3+ encoding"), _Switch(["-A", "A"], "Do not skip anomalous read pairs in variant calling."), _Option(["-b", "b"], "List of input BAM files, one file per line", filename=True, equate=False, checker_function=lambda x: isinstance(x, str)), _Option(["-d", "d"], "At a position, read maximally INT reads per input BAM", equate=False, checker_function=lambda x: isinstance(x, int)), _Switch(["-D", "D"], "Output per-sample read depth"), _Switch(["-S", "S"], """Output per-sample Phred-scaled strand bias P-value"""), _Option(["-e", "e"], """Phred-scaled gap extension sequencing error probability. Reducing INT leads to longer indels""", equate=False, checker_function=lambda x: isinstance(x, int)), _Option(["-h", "h"], """Coefficient for modeling homopolymer errors. Given an l-long homopolymer run, the sequencing error of an indel of size s is modeled as INT*s/l""", equate=False, checker_function=lambda x: isinstance(x, int)), _Switch(["-I", "I"], "Do not perform INDEL calling"), _Option(["-L", "L"], """Skip INDEL calling if the average per-sample depth is above INT""", equate=False, checker_function=lambda x: isinstance(x, int)), _Option(["-o", "o"], """Phred-scaled gap open sequencing error probability. Reducing INT leads to more indel calls.""", equate=False, checker_function=lambda x: isinstance(x, int)), _Option(["-p", "p"], """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 ILLUMINA""", equate=False, checker_function=lambda x: isinstance(x, str)), _ArgumentList(["input_file"], "Input File for generating mpileup", filename=True, is_required=True), ] AbstractCommandline.__init__(self, cmd, **kwargs)
def __init__(self, *args, cmd='mugsy', **kwargs): """ . """ self.parameters = [ _Option( ['--prefix', 'prefix'], 'prefix for output files', filename=True, equate=False, ), _Option( ['--directory', 'directory'], ('directory used to store output and temporary' 'files. Must be a absolute path'), filename=True, equate=False, ), _Option( ['--minlength', 'minlength'], ('minimum span of an aligned region in a colinear\n' 'block (bp). This is used by the segmentation step\n' 'synchain-mugsy. Default is 30bp.'), checker_function=lambda x: isinstance(x, int), equate=False, ), _Option( ['--duplications', 'duplications'], '1 - Detect and report duplications. 0 - Skip. Default is 0.', checker_function=lambda x: x in (0, 1), equate=False, ), _Option( ['--nucmeropts', 'nucmeropts'], ('options passed through to the Nucmer\n' 'package. Eg. -nucmeropts "-l 15" sets the minimum MUM length\n' 'in NUCmer to 15. See the Nucmer documentation at\n' 'http://mummer.sf.net for more information. Default is -l 15.'), checker_function=lambda x: "'" in x or '"' in x, equate=False, ), _Switch( ['-allownestedlcbs', 'allownestedlcbs'], ('Default=false. Places each multi-genome anchor\n' 'in exactly one LCB; the longest spanning LCB'), ), _Switch( ['-plot', 'plot'], ('output genome dot plots in GNUplot format. Overlays LCBS\n' 'onto pairwise plots from mummerplot. Display of draft\n' 'genomes in these plots is not supported.'), ), _Switch( ['-fullsearch', 'fullsearch'], ('Run a complete all pairs Nucmer search with each \n' 'sequence as a reference and query (n^2-1 total searches).\n' 'Default is one direction only (n^2-1/2 searches).'), ), _Option( ['-refine', 'refine'], ('run an second iteration of Mugsy on each LCB to refine the \n' 'alignment using either Mugsy (--refine mugsy), FSA (--refine\n' 'fsa), Pecan (--refine pecan), MLAGAN (--refine mlagan).\n' 'Requires necessary tools are in your path:\n' 'fsa: fsa\n' 'pecan: muscle,exonerate, in the path. classpath set ' 'for bp.pecan.Pecan.\n' 'mlagan: mlagan.sh'), checker_function=lambda x: x in ('mugsy', 'fsa', 'pecan', 'mlagan'), equate=False, ), _ArgumentList( ['input'], ('Input is one or more (multi)FASTA files, one per genome.\n' 'Each file should contain all the sequences for a single\n' 'organism/species. The filename is used as the genome name.\n' '\n' 'Limitations on FASTA input: input FASTA headers must\n' "not contain ':' or '-' ambiguity characters are converted \n" 'to N in output'), filename=True, is_required=True, ) ] AbstractCommandline.__init__(self, cmd, **kwargs)