dae.utils package
Submodules
dae.utils.dae_utils module
- dae.utils.dae_utils.cshl2vcf_variant(location: str, variant: str, genome: ReferenceGenome) tuple[str, int, str, str] [source]
- dae.utils.dae_utils.dae2vcf_variant(chrom: str, position: int, variant: str, genome: ReferenceGenome) tuple[int, str, str] [source]
Convert a given CSHL-style variant to the VCF format.
dae.utils.debug_closing module
- class dae.utils.debug_closing.closing(thing)[source]
Bases:
AbstractContextManager
Context to automatically close something at the end of a block.
Code like this:
- with closing(<module>.open(<arguments>)) as f:
<block>
is equivalent to this:
f = <module>.open(<arguments>) try:
<block>
- finally:
f.close()
dae.utils.dict_utils module
dae.utils.effect_utils module
dae.utils.filehash module
dae.utils.fixtures module
dae.utils.fs_utils module
- dae.utils.fs_utils.containing_path(path: str | PathLike) str [source]
Return url to the resource that contains path.
For file paths this is equivalent to the containing directory. For urls this is equivalent to the containing resource.
- dae.utils.fs_utils.find_directory_with_a_file(filename: str, cwd: str | Path | None = None) Path | None [source]
Find a directory containing a file.
Starts from current working directory or from a directory passed.
- dae.utils.fs_utils.modified(filename: str) datetime [source]
Return the modified timestamp of a file.
dae.utils.helpers module
- dae.utils.helpers.convert_size(size_bytes: int) str [source]
Convert an integer representing size in bytes to a human-readable string.
Copied from: https://stackoverflow.com/questions/5194057/better-way-to-convert-file-sizes-in-python
dae.utils.progress module
dae.utils.regions module
- class dae.utils.regions.BedRegion(chrom: str, start: int, stop: int)[source]
Bases:
Region
Represents proper bed regions.
- property begin: int
- property end: int
- property start: int
- property stop: int
- class dae.utils.regions.Region(chrom: str, start: int | None = None, stop: int | None = None)[source]
Bases:
object
Class representing a genomic region.
- property begin: int | None
- property end: int | None
- intersection(other: Region) Region | None [source]
Return intersection of the region with other region.
- property start: int | None
- property stop: int | None
- dae.utils.regions.all_regions_from_chrom(regions: list[dae.utils.regions.Region], chrom: str) list[dae.utils.regions.Region] [source]
Subset of regions in R that are from chr.
- dae.utils.regions.bedfile2regions(bed_filename: str) list[dae.utils.regions.BedRegion] [source]
Transform BED file into list of regions.
- dae.utils.regions.collapse(source: Sequence[Region], is_sorted: bool = False) list[dae.utils.regions.Region] [source]
Collapse list of regions.
- dae.utils.regions.collapse_no_chrom(source: list[dae.utils.regions.BedRegion], is_sorted: bool = False) list[dae.utils.regions.BedRegion] [source]
Collapse by ignoring the chromosome.
Useful when the caller knows that all the regions are from the same chromosome.
- dae.utils.regions.connected_component(regions: list[dae.utils.regions.BedRegion]) Any [source]
Return connected component of regions.
This might be the same as collapse.
- dae.utils.regions.difference(regions1: list[dae.utils.regions.Region], regions2: list[dae.utils.regions.Region], symmetric: bool = False) list[dae.utils.regions.Region] [source]
Compute difference between two list of regions.
- dae.utils.regions.get_chromosome_length_tabix(tabix_file: TabixFile | VariantFile, chrom: str, step: int = 100000000, precision: int = 5000000) int | None [source]
Return the length of a chromosome (or contig).
Returned value is guarnteed to be larger than the actual contig length.
- dae.utils.regions.intersection(regions1: list[dae.utils.regions.Region], regions2: list[dae.utils.regions.Region]) list[dae.utils.regions.Region] [source]
Compute intersection of two list of regions.
First collapses each for lists of regions s1 and s2 and then find the intersection.
- dae.utils.regions.regions2bedfile(regions: list[dae.utils.regions.BedRegion], bed_filename: str) None [source]
Save list of regions into a BED file.
- dae.utils.regions.split_into_regions(chrom: str, chrom_length: int, region_size: int) list[dae.utils.regions.Region] [source]
Return a list of regions for a chrom with a given length.
- dae.utils.regions.total_length(regions: list[dae.utils.regions.BedRegion]) int [source]
- dae.utils.regions.union(*r: list[dae.utils.regions.Region]) list[dae.utils.regions.Region] [source]
Collapse many lists of regions.
- dae.utils.regions.unique_regions(regions: list[dae.utils.regions.Region]) list[dae.utils.regions.Region] [source]
Remove duplicated regions.
dae.utils.sql_utils module
dae.utils.statistics module
- class dae.utils.statistics.StatsCollection[source]
Bases:
MutableMapping
Helper class for collection of variuos statistics.
This class would be used in the project in places where collection of statistics data about how components of the system work seems appropriate.
It provides a dict-like interface.
The keys are tuples of strings. The values could be anything, but usually they are numbers.
>>> stats = StatsCollection() >>> stats[("a",)] = 1 >>> stats[("a",)] 1 >>> stats.get(("a", 1))
The keys a treated as a hierarchy. You can get all values whose key’s start match the passed key. For example if you add following: >>> stats[(“b”, “1”)] = 42 >>> stats[(“b”, “2”)] = 43
you can get all values whose keys start with (“b”,…) using: >>> stats[(“b”,)] {(‘b’, ‘1’): 42, (‘b’, ‘2’): 43}
dae.utils.variant_utils module
- dae.utils.variant_utils.best2gt(best_state: ~numpy.ndarray, dtype: ~numpy.dtype[~typing.Any] | None | type[typing.Any] | ~numpy._typing._dtype_like._SupportsDType[~numpy.dtype[~typing.Any]] | str | tuple[typing.Any, int] | tuple[typing.Any, typing.Union[typing.SupportsIndex, collections.abc.Sequence[typing.SupportsIndex]]] | list[typing.Any] | ~numpy._typing._dtype_like._DTypeDict | tuple[typing.Any, typing.Any] = <class 'numpy.int8'>) ndarray [source]
Convert a best state array to a genotype array.
- dae.utils.variant_utils.fgt2str(family_genotypes: ndarray, sep: str = ';') str [source]
Convert a family genotype array to a string.
- dae.utils.variant_utils.get_interval_locus_ploidy(chrom: str, pos_start: int, pos_end: int, sex: Sex, genome: ReferenceGenome) int [source]
- dae.utils.variant_utils.get_locus_ploidy(chrom: str, pos: int, sex: Sex, genome: ReferenceGenome) int [source]
- dae.utils.variant_utils.str2fgt(fgt: str) ndarray [source]
Convert a string to a family genotype array.
- dae.utils.variant_utils.str2gt(genotypes: str, split: str = ', ', dtype: ~numpy.dtype[~typing.Any] | None | type[typing.Any] | ~numpy._typing._dtype_like._SupportsDType[~numpy.dtype[~typing.Any]] | str | tuple[typing.Any, int] | tuple[typing.Any, typing.Union[typing.SupportsIndex, collections.abc.Sequence[typing.SupportsIndex]]] | list[typing.Any] | ~numpy._typing._dtype_like._DTypeDict | tuple[typing.Any, typing.Any] = <class 'numpy.int8'>) ndarray [source]
Convert a string to a genotype array.
- dae.utils.variant_utils.str2mat(mat: str, col_sep: str = '', row_sep: str = '/', dtype: ~numpy.dtype[~typing.Any] | None | type[typing.Any] | ~numpy._typing._dtype_like._SupportsDType[~numpy.dtype[~typing.Any]] | str | tuple[typing.Any, int] | tuple[typing.Any, typing.Union[typing.SupportsIndex, collections.abc.Sequence[typing.SupportsIndex]]] | list[typing.Any] | ~numpy._typing._dtype_like._DTypeDict | tuple[typing.Any, typing.Any] = <class 'numpy.int8'>) ndarray [source]
Convert a string into a numpy matrix.
- dae.utils.variant_utils.str2mat_adjust_colsep(mat: str) ndarray [source]
Convert a string into a numpy matrix.
- dae.utils.variant_utils.trim_parsimonious(pos: int, ref: str, alt: str) tuple[int, str, str] [source]
Trim identical nucleotides on both ends and adjust position.
- dae.utils.variant_utils.trim_str_left(pos: int, ref: str, alt: str) tuple[int, str, str] [source]
Trim identical nucleotides prefixes and adjust position accordingly.
- dae.utils.variant_utils.trim_str_left_right(pos: int, ref: str, alt: str) tuple[int, str, str] [source]
dae.utils.verbosity_configuration module
Provides common configuration for loggers verbosity.
- class dae.utils.verbosity_configuration.VerbosityConfiguration[source]
Bases:
object
Defines common configuration of verbosity for loggers.
- static set(args: Namespace) None [source]
Read verbosity settings from parsed arguments and sets logger.