I/O Module
Classes
BedSet(region_sets=None, file_path=None, identifier=None)
BedSet object
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
region_sets
|
Union[List[RegionSet], List[str], List[List[Region]], None]
|
list of BED file paths, RegionSet, or 2-dimension list of Region [Default: None - empty BedSet] |
None
|
file_path
|
str
|
path to the .txt file with identifier of all BED files in it |
None
|
identifier
|
str
|
the identifier of the BED set |
None
|
Functions
add(bedfile)
Add a BED file to the BED set
!Warning: if new bedfile will be added, bedSet identifier will be changed!
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
bedfile
|
RegionSet
|
RegionSet instance, that should be added to the bedSet |
required |
Returns:
| Type | Description |
|---|---|
NoReturn
|
NoReturn |
to_granges_list()
Process a list of BED set identifiers and returns a GenomicRangesList object
compute_bedset_identifier()
Return the identifier. If it is not set, compute one
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
bedset
|
BedSet object |
required |
Returns:
| Type | Description |
|---|---|
str
|
the identifier of BED set |
RegionSet(regions, backed=False)
Instantiate a RegionSet object. This can be backed or not backed. It represents a set of genomic regions.
If you specify backed as True, then the bed file will not be loaded into memory. This is useful for large
bed files. You can still iterate over the regions, but you cannot index into them.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
regions
|
Union[str, List[Region]]
|
path, or url to bed file or list of Region objects |
required |
backed
|
bool
|
whether to load the bed file into memory or not [Default: False] |
False
|
Functions
to_granges()
Return GenomicRanges contained in this BED file
Returns:
| Type | Description |
|---|---|
GenomicRanges
|
GenomicRanges object |
compute_bed_identifier()
Return bed file identifier. If it is not set, compute one
Returns:
| Type | Description |
|---|---|
str
|
the identifier of BED file (str) |
Region(chr, start, stop)
Instantiate a Region object.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
chr
|
str
|
chromosome |
required |
start
|
int
|
start position |
required |
stop
|
int
|
stop position |
required |