evidence module

class mavis.validate.evidence.GenomeEvidence(*pos, **kwargs)

Bases: mavis.validate.base.Evidence

compute_fragment_size(read, mate=None)

class mavis.validate.evidence.TranscriptomeEvidence(annotations, *pos, **kwargs)

Bases: mavis.validate.base.Evidence

static compute_exonic_distance(start, end, transcripts)

give the current list of transcripts, computes the putative exonic/intergenic distance given two genomic positions. Intronic positions are ignored

compute_fragment_size(read, mate)

static traverse_exonic_distance(start, distance, direction, transcripts)

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

Parameters:

• 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
• transcripts (list of UsTranscript) – list of transcripts to use