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):
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)
