read module

mavis.bam.read.breakpoint_pos(read, orient='?')[source]

assumes the breakpoint is the position following softclipping on the side with more softclipping (unless and orientation has been specified)

Parameters:
Returns:

the position of the breakpoint in the input read
Return type:

int
mavis.bam.read.calculate_alignment_score(read)[source]

calculates a score for comparing alignments

Parameters:read (pysam.AlignedSegment) – the input read
Returns:the score
Return type:float
mavis.bam.read.nsb_align(ref, seq, weight_of_score=0.5, min_overlap_percent=1, min_match=0, scoring_function=<function calculate_alignment_score>)[source]

given some reference string and a smaller sequence string computes the best non-space-breaking alignment i.e. an alignment that does not allow for indels (straight-match). Positions in the aligned segments are given relative to the length of the reference sequence (1-based)

Parameters:
  • ref (str) – the reference sequence
  • seq (str) – the sequence being aligned
  • weight_of_score (float) – when scoring alignments this determines the amount of weigth to place on the cigar match. Should be a number between 0 and 1
  • min_overlap_percent (float) – the minimum amount of overlap of the input sequence to the reference should be a number between 0 and 1
  • min_match (float) – the minimum number of matches compared to total
  • scoring_function (callable) – any function that will take a read as input and return a float used in comparing alignments to choose the best alignment
Returns:

list of aligned segments
Return type:

list of AlignedSegment

Note

using a higher min_match may improve performance as low quality alignments are rejected more quickly. However this may also result in no match being returned when there is no high quality match to be found.

mavis.bam.read.orientation_supports_type(read, event_type)[source]

checks if the orientation is compatible with the type of event

Parameters:
Returns:

  • True - the read pair is in the correct orientation for this event type
  • False - the read is not in the correct orientation
Return type:

bool
mavis.bam.read.read_pair_type(read)[source]

assumptions based on illumina pairs: only 4 possible combinations

Parameters:read (AlignedSegment) – the input read
Returns:the type of input read pair
Return type:READ_PAIR_TYPE
Raises:NotImplementedError – for any read that does not fall into the four expected configurations (see below) 
++++> <---- is LR same-strand
++++> ++++> is LL opposite
<---- <---- is RR opposite
<---- ++++> is RL same-strand
mavis.bam.read.sequenced_strand(read, strand_determining_read=2)[source]

determines the strand that was sequenced

Parameters:
  • read (AlignedSegment) – the read being used to determine the strand
  • strand_determining_read (int) – which read in the read pair is the same as the sequenced strand
Returns:

the strand that was sequenced
Return type:

STRAND
Raises:

ValueError – if strand_determining_read is not 1 or 2

Warning

if the input pair is unstranded the information will not be representative of the strand sequenced since the assumed convention is not followed