mavis.validate.evidence
class mavis.validate.evidence.GenomeEvidence
inherits Evidence
mavis.validate.evidence.GenomeEvidence.generate_window()
given some input breakpoint uses the current evidence setting to determine an appropriate window/range of where one should search for supporting reads
def generate_window(self, breakpoint):
Args
- breakpoint (
Breakpoint
): the breakpoint we are generating the evidence window for
Returns
Interval
: the range where reads should be read from the bam looking for evidence for this event
class mavis.validate.evidence.TranscriptomeEvidence
inherits Evidence
mavis.validate.evidence.TranscriptomeEvidence.traverse()
given some genomic position and a distance. Uses the input transcripts to compute all possible genomic end positions at that distance if intronic positions are ignored
def traverse(self, start, distance, direction, strand=STRAND.NS, chrom=None):
Args
- start (
int
): the genomic start position - distance (
int
): the amount of exonic/intergenic units to traverse - direction (
ORIENT
): the direction wrt to the positive/forward reference strand to traverse - strand
- chrom
mavis.validate.evidence.TranscriptomeEvidence.distance()
give the current list of transcripts, computes the putative exonic/intergenic distance given two genomic positions. Intronic positions are ignored
Intergenic calculations are only done if exonic only fails
def distance(self, start, end, strand=STRAND.NS, chrom=None):
Args
- start
- end
- strand
- chrom
mavis.validate.evidence.TranscriptomeEvidence.generate_window()
given some input breakpoint uses the current evidence setting to determine an appropriate window/range of where one should search for supporting reads
def generate_window(self, breakpoint):
Args
- breakpoint (
Breakpoint
): the breakpoint we are generating the evidence window for
Returns
Interval
: the range where reads should be read from the bam looking for evidence for this event
mavis.validate.evidence.TranscriptomeEvidence.exon_boundary_shift_cigar()
given an input read, converts deletions to N when the deletion matches the exon boundaries. Also shifts alignments to correspond to the exon boundaries where possible
def exon_boundary_shift_cigar(self, read):
Args
- read