base module

class mavis.validate.base.Evidence(break1, break2, bam_cache, REFERENCE_GENOME, read_length, stdev_fragment_size, median_fragment_size, stranded=False, opposing_strands=None, untemplated_seq=None, data={}, classification=None, **kwargs)

Bases: mavis.breakpoint.BreakpointPair

Parameters:

• breakpoint_pair (BreakpointPair) – the breakpoint pair to collect evidence for
• bam_cache (BamCache) – the bam cache (and assc file) to collect evidence from
• REFERENCE_GENOME (dict of Bio.SeqRecord by str) – dict of reference sequence by template/chr name
• data (dict) – a dictionary of data to associate with the evidence object
• classification (SVTYPE) – the event type
• protocol (PROTOCOL) – genome or transcriptome

assemble_contig(log=<function Evidence.<lambda>>)

uses the split reads and the partners of the half mapped reads to create a contig representing the sequence across the breakpoints

if it is not strand specific then sequences are sorted alphanumerically and only the first of a pair is kept (paired by sequence)

collect_compatible_flanking_pair(read, mate, compatible_type)

collect_flanking_pair(read, mate)

checks if a given read meets the minimum quality criteria to be counted as evidence as stored as support for this event

Parameters:read (pysam.AlignedSegment) – the read to add Raises:UserWarning – the read does not support this event or does not pass quality filters

see theory - types of flanking evidence

collect_spanning_read(read)

spanning read: a read covering BOTH breakpoints

This is only applicable to small events. Do not need to look for soft clipped reads here since they will be collected already

collect_split_read(read, first_breakpoint)

adds a split read if it passes the criteria filters and raises a warning if it does not

Parameters:

• read (pysam.AlignedSegment) – the read to add
• first_breakpoint (bool) – add to the first breakpoint (or second if false)

Raises:

• UserWarning – the read does not support this breakpoint or does not pass quality filters
• AttributeError – orientation wasn’t specified for the breakpoint

compute_fragment_size(read, mate)

copy()

decide_sequenced_strand(reads)

flatten()

get_bed_repesentation()

inner_window1

Interval – the window where evidence will be gathered for the first breakpoint

inner_window2

Interval – the window where evidence will be gathered for the second breakpoint

load_evidence(log=<function Evidence.<lambda>>)

open the associated bam file and read and store the evidence does some preliminary read-quality filtering

Todo

support gathering evidence for small structural variants

max_expected_fragment_size

min_expected_fragment_size

outer_window1

Interval – the window where evidence will be gathered for the first breakpoint

see theory - calculating the evidence window

outer_window2

Interval – the window where evidence will be gathered for the second breakpoint

see theory - calculating the evidence window

putative_event_types()

standardize_read(read)

supporting_reads()

convenience method to return all flanking, split and spanning reads associated with an evidence object