oakvar.api

license

license(outer=None)

Shows the OakVar license information.

run

run(
    inputs,
    annotators=[],
    report_types=[],
    reports=[],
    annotators_replace=[],
    excludes=[],
    run_name=[],
    output_dir=[],
    startat=None,
    endat=None,
    skip=[],
    confpath=None,
    conf={},
    genome=None,
    cleandb=False,
    newlog=False,
    note="",
    mp=None,
    keep_temp=False,
    writeadmindb=False,
    job_name=None,
    separatesample=False,
    primary_transcript=["mane"],
    clean=False,
    module_options={},
    system_option={},
    package=None,
    filtersql=None,
    includesample=None,
    excludesample=None,
    filter=None,
    filterpath=None,
    modules_dir=None,
    preparers=[],
    mapper_name=[],
    postaggregators=[],
    vcf2vcf=False,
    logtofile=False,
    loglevel="INFO",
    combine_input=False,
    input_format=None,
    converter_module=None,
    input_encoding=None,
    ignore_sample=False,
    uid=None,
    skip_variant_deduplication=False,
    loop=None,
    outer=None,
)

Performs OakVar pipeline from conversion -> mapping -> annotation -> database generation -> post annotation -> report generation.

PARAMETER	DESCRIPTION
`inputs`	Paths to input files. URLs can be used as well, in which the files will be downloaded. TYPE: `List[Union[Path, str]]`
`combine_input`	If True, all input files will be combined as one input. TYPE: `bool` DEFAULT: `False`
`annotators`	Annotator modules to run TYPE: `List[str]` DEFAULT: `[]`
`report_types`	Report types. If given, report files of given types will be generated. If `vcfreporter` is installed in your system, giving `vcf` will invoke the module. TYPE: `Union[str, List[str]]` DEFAULT: `[]`
`clean`	Cleans all output and intermediate files and then starts the pipeline. TYPE: `bool` DEFAULT: `False`
`vcf2vcf`	If True, the pipeline will run in vcf2vcf mode, where input and output should be VCF format files and result database files will not be generated. This can increase the speed of the pipeline significantly. TYPE: `bool` DEFAULT: `False`
`logtofile`	If True, .log and .err log files will be generated for normal and error logs. TYPE: `bool` DEFAULT: `False`
`input_format`	Overrides automatic detection of input file format. TYPE: `Optional[str]` DEFAULT: `None`
`postaggregators`	Postaggregator modules to run TYPE: `List[str]` DEFAULT: `[]`
`preparers`	Preparer modules to run TYPE: `List[str]` DEFAULT: `[]`
`mapper_name`	Mapper module to run TYPE: `List[str]` DEFAULT: `[]`
`output_dir`	Output directories. The order of inputs and output_dir elements should match. TYPE: `List[str]` DEFAULT: `[]`
`startat`	Start at the specified step. Options are `converter`, `mapper`, `annotator`, `aggregator`, `postaggregator`, and `reporter`. TYPE: `Optional[str]` DEFAULT: `None`
`endat`	End at the specified step. Options are `converter`, `mapper`, `annotator`, `aggregator`, `postaggregator`, and `reporter`. TYPE: `Optional[str]` DEFAULT: `None`
`skip`	Skip the specified steps. Options are `converter`, `mapper`, `annotator`, `aggregator`, `postaggregator`, and `reporter`. TYPE: `List[str]` DEFAULT: `[]`
`genome`	Genome assembly of all input files. If not given, genome assembly will be figured out or default to what is defined in lib/system/consts.py:default_assembly. TYPE: `Optional[str]` DEFAULT: `None`
`input_encoding`	input_encoding TYPE: `Optional[str]` DEFAULT: `None`
`converter_module`	converter module folder path TYPE: `Optional[str]` DEFAULT: `None`
`mp`	Number of cores to use. Default value can be changed by `ov config system max_num_concurrent_annotators_per_job <value>`. TYPE: `Optional[int]` DEFAULT: `None`
`primary_transcript`	primary_transcript TYPE: `List[str]` DEFAULT: `['mane']`
`modules_dir`	modules_dir TYPE: `Optional[str]` DEFAULT: `None`
`run_name`	run_name TYPE: `List[str]` DEFAULT: `[]`
`annotators_replace`	annotators_replace TYPE: `List[str]` DEFAULT: `[]`
`excludes`	excludes TYPE: `List[str]` DEFAULT: `[]`
`confpath`	confpath TYPE: `Optional[str]` DEFAULT: `None`
`conf`	conf TYPE: `dict` DEFAULT: `{}`
`cleandb`	cleandb TYPE: `bool` DEFAULT: `False`
`newlog`	newlog TYPE: `bool` DEFAULT: `False`
`note`	note TYPE: `str` DEFAULT: `''`
`keep_temp`	keep_temp TYPE: `bool` DEFAULT: `False`
`writeadmindb`	writeadmindb TYPE: `bool` DEFAULT: `False`
`job_name`	job_name TYPE: `Optional[List[str]]` DEFAULT: `None`
`separatesample`	separatesample TYPE: `bool` DEFAULT: `False`
`module_options`	module_options TYPE: `Dict` DEFAULT: `{}`
`system_option`	system_option TYPE: `Dict` DEFAULT: `{}`
`package`	package TYPE: `Optional[str]` DEFAULT: `None`
`filtersql`	filtersql TYPE: `Optional[str]` DEFAULT: `None`
`includesample`	includesample TYPE: `Optional[List[str]]` DEFAULT: `None`
`excludesample`	excludesample TYPE: `Optional[List[str]]` DEFAULT: `None`
`filter`	filter TYPE: `Optional[str]` DEFAULT: `None`
`filterpath`	filterpath TYPE: `Optional[str]` DEFAULT: `None`
`loglevel`	loglevel TYPE: `str` DEFAULT: `'INFO'`
`uid`	uid TYPE: `Optional[str]` DEFAULT: `None`
`skip_variant_deduplication`	Skip de-duplication of variants. TYPE: `bool` DEFAULT: `False`
`loop`	DEFAULT: `None`
`outer`	DEFAULT: `None`

RETURNS	DESCRIPTION
`Optional[Dict[str, Any]]`	None or a dict of reporter names and their return values

report

report(
    dbpath,
    report_types=None,
    module_paths=None,
    filterpath=None,
    filter=None,
    filtersql=None,
    filtername=None,
    filterstring=None,
    savepath=None,
    confpath=None,
    conf={},
    nogenelevelonvariantlevel=False,
    inputfiles=None,
    separatesample=False,
    output_dir=None,
    run_name="",
    includesample=[],
    excludesample=None,
    package=None,
    cols=None,
    level=None,
    user=None,
    no_summary=False,
    serveradmindb=None,
    module_options={},
    head_n=None,
    logtofile=False,
    outer=None,
    loop=None,
)

Generates OakVar report files based on an OakVar result database file.

PARAMETER	DESCRIPTION
`dbpath`	Path to an OakVar result database file TYPE: `str`
`report_types`	Report types. For example, if `vcfreporter` module is installed, `"vcf"` will invoke the reporter. TYPE: `Optional[Union[str, List[str]]]` DEFAULT: `None`
`module_paths`	Paths to report modules can be directly given. This option will override report_types. For example, if `customreporter` module is installed at `/home/user/ov_dev/customreporter`, this value can be given. TYPE: `Union[str, List[Path]]` DEFAULT: `None`
`output_dir`	Directory to store reports TYPE: `Optional[str]` DEFAULT: `None`
`module_options`	Reporter module-specific options. For example, to tell `vcfreporter` to combine all OakVar result fields under one field, `{"vcfreporter": {"type": "combined"}}` can be used. TYPE: `Dict[str, Dict]` DEFAULT: `{}`
`cols`	Result columns to include. By default, all result columns are included in reports. For example, `["base__uid", "base__chrom", "base__pos", "base__ref_base", "base__alt_base", "clinvar__sig"]` will include only the variants and ClinVar significances. TYPE: `Optional[List[str]]` DEFAULT: `None`
`includesample`	Samples to include in filtered reports TYPE: `Optional[List[str]]` DEFAULT: `[]`
`excludesample`	Samples to exclude from filtered reports TYPE: `Optional[List[str]]` DEFAULT: `None`
`filterpath`	filterpath TYPE: `Optional[str]` DEFAULT: `None`
`filter`	filter as dict TYPE: `Optional[dict]` DEFAULT: `None`
`filtersql`	filter sql TYPE: `Optional[str]` DEFAULT: `None`
`filtername`	filter file TYPE: `Optional[str]` DEFAULT: `None`
`filterstring`	filter dict as str TYPE: `Optional[str]` DEFAULT: `None`
`savepath`	savepath TYPE: `Optional[Path]` DEFAULT: `None`
`confpath`	confpath TYPE: `Optional[str]` DEFAULT: `None`
`nogenelevelonvariantlevel`	nogenelevelonvariantlevel TYPE: `bool` DEFAULT: `False`
`inputfiles`	inputfiles TYPE: `Optional[List[str]]` DEFAULT: `None`
`separatesample`	separatesample TYPE: `bool` DEFAULT: `False`
`package`	package TYPE: `Optional[str]` DEFAULT: `None`
`modules_dir`	modules_dir TYPE: `Optional[str]`
`level`	level TYPE: `Optional[str]` DEFAULT: `None`
`user`	user TYPE: `Optional[str]` DEFAULT: `None`
`no_summary`	no_summary TYPE: `bool` DEFAULT: `False`
`head_n`	Make a report with the first n number of variants. TYPE: `Optional[int]` DEFAULT: `None`
`serveradmindb`	DEFAULT: `None`
`outer`	DEFAULT: `None`
`loop`	DEFAULT: `None`

RETURNS	DESCRIPTION
`Dict[str, Any]`	None or a dict of reporter names and their return values

report_issue

report_issue()

Opens a webpage to report issues.

update

update(outer=None)

Updates OakVar to the latest version and sets up OakVar again.

PARAMETER	DESCRIPTION
`outer`	DEFAULT: `None`

RETURNS	DESCRIPTION
`bool`	`True` if successful, `False` if not.

version

version()

Gets OakVar version.