SubGraph

class gratools.Graph.SubGraph(bam_path: pathlib.Path, bed_path: pathlib.Path, logger: logging.Logger = <factory>, sample_name: str = None, chromosome: str = None, start: int = None, stop: int = None, intersect_bed: pybedtools.bedtool.BedTool = None, segment_id_set: set = <factory>, segment_id_first: str = None, segment_id_last: str = None, gfa_walk_list: list = <factory>, gfa_link_list: list = <factory>, gfa_segment_list: list = <factory>, dict_segments_samples: collections.defaultdict = <factory>, dict_segments_sequence: collections.defaultdict = <factory>, sequences_list: list = <factory>)[source]

Bases: object

Attributes Summary

`chromosome`
`intersect_bed`
`progress`
`sample_name`
`segment_id_first`
`segment_id_last`
`start`
`stop`
`task_id`

Methods Summary

`build_fasta`()
`build_segments`()
`build_walks`()	Build the walks from the intersected BED regions.
`compute_intersection`([list_chromosomes])	Compute the intersection of BED regions.
`get_chr_pos`(progress, task_id)

Attributes Documentation

chromosome: str = None

intersect_bed: BedTool = None

progress = None

sample_name: str = None

segment_id_first: str = None

segment_id_last: str = None

start: int = None

stop: int = None

task_id = None

Methods Documentation

build_fasta()[source]

build_segments()[source]

build_walks()[source]: Build the walks from the intersected BED regions.

compute_intersection(list_chromosomes=None)[source]: Compute the intersection of BED regions.

get_chr_pos(progress, task_id)[source]