GratoolsBam

class gratools.Graph.GratoolsBam(bam_path: ~pathlib.Path, threads: int = 1, logger: ~logging.Logger = <factory>)

Bases: object

Class for handling BAM files.

Attributes Summary

threads

Methods Summary

build_segments([list_segments])	Extract segments from a BAM file.
index_bam()	Indexes the BAM file specified by self.bam_path.
segments_info(output_base_path, nb_samples_gfa)
specific_and_shared_segments([...])
tag(dict_link_SA_SB, dict_segments_samples)	Add tags to the BAM file with the given dictionary data.

Attributes Documentation

threads: int = 1

Methods Documentation

build_segments(list_segments: list | None = None)

Extract segments from a BAM file.

Parameters:

list_segments (list) – A list of segment IDs to extract from the BAM file.

Returns:

A tuple containing the GFA segments list, segment samples dictionary, and segment sequence dictionary.

Return type:

tuple

index_bam()

Indexes the BAM file specified by self.bam_path.

Parameters:

self (object) – The instance of the class.

Returns:

None

segments_info(output_base_path, nb_samples_gfa, shared_min=1, specific_max=None, filter_len=1)

specific_and_shared_segments(samples_list_A=None, samples_list_B=None, filter_len=None)

tag(dict_link_SA_SB: dict, dict_segments_samples: dict)

Add tags to the BAM file with the given dictionary data.

Parameters:

• dict_link_SA_SB (dict) – Dictionary containing link information for SA and SB.

• dict_segments_samples (dict) – Dictionary containing segment samples.

Returns:

The path to the tagged segments BAM file.

Return type:

str