Bedpe

Constructor

Bedpe(df_svpos, odict_df_info[, patient_name])

Relational database-like object containing SV position dataframes and INFO dataframes.

Attributes

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

Annotation

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

Calculation

Bedpe.calculate_info(operation, name)

Calculate values of INFO tables according to the 'operation' argument and add a new INFO table as the result.

Conversion

Bedpe.copy()	Return copy of the instance
Bedpe.to_bedpe_like([custom_infonames, ...])	Return a DataFrame in bedpe-like format.

Export

Bedpe.to_bedpe(path_or_buf[, ...])

to_beddpe(path_or_buf, custom_infonames, confidence_intervals) Return a BEDPE file.

Filtering

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

Managing Tables

Bedpe.append_infos(base_df, ls_tablenames[, ...])	Append INFO tables to the right of the base_df, based on the SV id columns.
Bedpe.get_table(table_name)	Return a table specified in the argument as pandas DataFrame object.
Bedpe.add_info_table(table_name, df)	Add a new INFO table to self.
Bedpe.remove_info_table(table_name)	Remove an INFO table from self.
Bedpe.rename_info(table_name, value[, ...])	Rename INFO name of this object.
Bedpe.replace_table(table_name, table)	Replace existing table into new table.
Bedpe.set_value_for_info_by_id(table_name, ...)	Set value to the specified info table by sv_id.

Merging

Bedpe.merge(ls_bedpe, ls_caller_names, threshold)

Return a merged bedpe object from mulitple caller's bedpe objects in ls_bedpe

Representation

Bedpe.view(custom_infonames, return_as_dataframe)

Quick view function of the Vcf object.

Signature_analysis

Bedpe.classify_manual_svtype(definitions, ...)	Classify SV records by user-defined criteria.
Bedpe.get_feature_count_as_series(feature, ...)	Return counts of unique values as a pd.Series for the INFO specified in the "feature" argument.