summary module¶
-
mavis.summary.summary.
alphanumeric_choice
(bpp1, bpp2)[source]¶ Parameters: - bpp1 (BreakpointPair) –
- bpp2 (BreakpointPair) –
returns the one with transcript with alphanumeric priority, with transcript1 chosen for ties
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mavis.summary.summary.
filter_by_annotations
(bpp1, bpp2, best_transcripts)[source]¶ Parameters: - bpp1 (BreakPointPair) –
- bpp2 (BreakpointPair) –
- ( (best_transcripts) – class dict of
Transcript
bystr
): the best transcripts of the annotations based on their names
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mavis.summary.summary.
filter_by_evidence
(bpps, filter_min_remapped_reads=5, filter_min_spanning_reads=5, filter_min_flanking_reads=5, filter_min_flanking_only_reads=10, filter_min_split_reads=5, filter_min_linking_split_reads=1)[source]¶
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mavis.summary.summary.
get_pairing_state
(current_protocol, current_disease_state, other_protocol, other_disease_state, 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)