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, keep_liftover_failed=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(yes=False, 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.