MultiVcf

Constructor

MultiVcf([ls_vcf, ls_patient_names, ...])

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

Attributes

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

Accessing the Tables

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

Filtering

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

Adding Informations

MultiVcf.add_info_table(table_name, df)

Add a new INFO table to self.

Annotation

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

Conversion

MultiVcf.as_bedpe_multi()

Convert MultiVcf object into MultiBedpe object.

Representation

MultiVcf.view(custom_infonames, ...)

Quick view function of the Vcf object.

Signature_analysis

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