Vcf

Constructor

Vcf(df_svpos, df_filters, odict_df_info, ...)

Relational database-like object containing SV position dataframes, FILTER dataframe, INFO dataframes, FORMAT dataframe, and HEADER dataframes.

Attributes

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

Annotation

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

Conversion

Vcf.copy()	Return copy of the instance.
Vcf.to_bedpe_like([custom_infonames])	Return a DataFrame in bedpe-like format.
Vcf.as_bedpe()	Convert Vcf object into Bedpe object.
Vcf.to_vcf_like()	Return a vcf-formatted DataFrame.
Vcf.breakend2breakpoint()	Converts a Vcf object into a breakpoint-based Vcf object by integrating the paired breakends (BND) and infering their SVTYPE.

Export

Vcf.to_bedpe(file_or_buf[, ...])	to_bedpe_like(file_or_buf, custom_infonames=[], add_filters, add_formats, confidence_intervals: bool=False) Return a BEDPE file.
Vcf.to_vcf(path_or_buf)	Return a vcf-formatted String.

Filtering

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

Managing Tables

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

Merging

Vcf.merge(ls_vcf, ls_caller_names, threshold)	Return a merged or integrated vcf object from mulitple caller's bedpe objects in ls_bedpe
Vcf.integrate(merged_vcf, priority)	Return an integrated Vcf object

Representation

Vcf.view(custom_infonames, return_as_dataframe)

Quick view function of the Vcf object.

Signature_analysis

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

SV ID/SV records

Vcf.replace_svid(to_replace, value)	Renamed specified SV ID.
Vcf.drop_by_id(svid)	Remove SV records specified in "svid" argument.