summary module

mavis.summary.summary.alphanumeric_choice(bpp1, bpp2)[source]
Parameters:

returns the one with transcript with alphanumeric priority, with transcript1 chosen for ties

mavis.summary.summary.annotate_dgv(bpps, dgv_regions_by_reference_name, distance=0)[source]

given a list of bpps and a dgv reference, annotate the events that are within the set distance of both breakpoints

Parameters:
  • bpps (list) – the list of BreakpointPair objects
  • dgv_regions_by_reference_name (dict) – the dgv reference regions file loaded by load_masking_regions
  • distance (int) – the minimum distance required to match a dgv event with a breakpoint
mavis.summary.summary.filter_by_annotations(bpp1, bpp2, best_transcripts)[source]
Parameters:
  • bpp1 (BreakPointPair) –
  • bpp2 (BreakpointPair) –
  • ( (best_transcripts) – class dict of Transcript by str): the best transcripts of the annotations based on their names
mavis.summary.summary.filter_by_call_method(bpp1, bpp2)[source]
mavis.summary.summary.filter_by_evidence(bpps, filter_min_remapped_reads=5, filter_min_spanning_reads=5, filter_min_flanking_reads=10, filter_min_split_reads=5, filter_min_linking_split_reads=1)[source]
mavis.summary.summary.get_pairing_state(current_protocol, current_disease_state, other_protocol, other_disease_state, is_matched=False, inferred_is_matched=False)[source]

given two libraries, returns the appropriate descriptor for their matched state

Parameters:
  • current_protocol (PROTOCOL) – the protocol of the current library
  • current_disease_state (DISEASE_STATUS) – the disease status of the current library
  • other_protocol (PROTOCOL) – protocol of the library being comparing to
  • other_disease_state (DISEASE_STATUS) – disease status of the library being compared to
  • is_matched (bool) – True if the libraries are paired
Returns:

descriptor of the pairing of the two libraries
Return type:

(PAIRING_STATE)
mavis.summary.summary.group_events(bpp1, bpp2)[source]