modos.genomics.region#

Classes#

Region

Genomic region consisting of a chromosome (aka reference) name

Module Contents#

class modos.genomics.region.Region[source]#

Genomic region consisting of a chromosome (aka reference) name and a 0-indexed half-open coordinate interval. Note that the end may not be specified, in which it will be set to math.inf.

chrom: str[source]#

start: int[source]#

end: int | float[source]#

__post_init__()[source]#

to_htsget_query()[source]#

Serializes the region into an htsget URL query.

Example

>>> Region(chrom='chr1', start=0, end=100).to_htsget_query()
'referenceName=chr1&start=0&end=100'

to_tuple()[source]#

Return the region as a simple tuple.

Return type:: tuple[str, Optional[int], Optional[int]]

classmethod from_htsget_query(url)[source]#

Instantiate from an htsget URL query

Example

>>> Region.from_htsget_query(
...   "http://localhost/htsget/reads/ex/demo1?format=CRAM&referenceName=chr1&start=0"
... )
Region(chrom='chr1', start=0, end=inf)

Parameters:: url (str)

classmethod from_ucsc(ucsc)[source]#

Instantiate from a UCSC-formatted region string.

Example

>>> Region.from_ucsc('chr-1ba:10-320')
Region(chrom='chr-1ba', start=10, end=320)
>>> Region.from_ucsc('chr1:-320')
Region(chrom='chr1', start=0, end=320)
>>> Region.from_ucsc('chr1:10-')
Region(chrom='chr1', start=10, end=inf)
>>> Region.from_ucsc('chr1:10')
Region(chrom='chr1', start=10, end=inf)

Note

For more information about the UCSC coordinate system, see: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms

Parameters:: ucsc (str)
Return type:: Region

classmethod from_pysam(record)[source]#

Parameters:: record (pysam.VariantRecord | pysam.AlignedSegment)
Return type:: Region

overlaps(other)[source]#

Checks if other in self. This check if any portion of other overlaps with self.

Parameters:: other (Region)
Return type:: bool

contains(other)[source]#

Checks if other is fully contained in self.

Parameters:: other (Region)
Return type:: bool