MultiBedpe

Constructor

MultiBedpe([ls_bedpe, ls_patient_names, ...])

A database-like object that contains information of multiple BEDPE files.

Attributes

MultiBedpe.sv_count	Return number of SV records.
MultiBedpe.table_list	Return a list of names of all tables in the object.
MultiBedpe.ids	Return all SV ids as list.

Accessing the Tables

MultiBedpe.get_table(table_name)	Return a table specified in the argument as pandas DataFrame object.
MultiBedpe.to_bedpe_like([custom_infonames, ...])	Return a DataFrame in bedpe-like format.

Filtering

MultiBedpe.filter(ls_query, query_logic)	Filter Bedpe object by the list of queries.
MultiBedpe.filter_by_id(arrlike_id)	Filter MultiBedpe object according to the list of SV ids.

Adding Informations

MultiBedpe.add_info_table(table_name, df)

Add a new INFO table to self.

Annotation

MultiBedpe.annotate_bed(bed, annotation[, ...])	Annotate SV breakpoints using Bed class object.
MultiBedpe.get_microhomology(fasta[, max_homlen])	Infer microhomology length and sequence in each breakpoint.

Representation

MultiBedpe.view(custom_infonames, ...)

Quick view function of the Vcf object.

Signature_analysis

MultiBedpe.classify_manual_svtype(...[, ...])	Classify SV records by user-defined criteria.
MultiBedpe.get_feature_count_as_data_frame([...])