Source code for velocyto.segment_match

from typing import *
import velocyto as vcy


class SegmentMatch:
    __slots__ = ["segment", "feature", "is_spliced"]
    
    def __init__(self, segment: Tuple[int, int], feature: vcy.Feature, is_spliced: bool=False) -> None:
        self.segment = segment
        self.feature = feature
        self.is_spliced = is_spliced  # this is really BAM_CREF_SKIP
        
    @property
    def maps_to_intron(self) -> bool:
        return self.feature.kind == 105  # ord("i")

    @property
    def maps_to_exon(self) -> bool:
        return self.feature.kind == 101  # ord("e")

    @property
    def skip_makes_sense(self) -> bool:
        """If the SKIP in the segment matches some extremity of the feature and therefore can be interpreted as a splice event
        """
        if not self.is_spliced:
            return True  # NOTE: maybe here I should raise an error because the property is not supposed to be called
        else:
            if abs(self.feature.start - self.segment[0]) <= vcy.SPLIC_INACUR or abs(self.feature.end - self.segment[1]) <= vcy.SPLIC_INACUR:
                return True
            else:
                return False

    def __repr__(self) -> str:
        txt = "<SegmentMatch "
        if self.maps_to_intron:
            txt += 'intron '
        if self.maps_to_exon:
            txt += 'exon '
        if self.is_spliced:
            txt += "spliced"
        txt += f"\nSegmentPosition:{self.segment[0]}-{self.segment[1]} ({self.segment[1]-self.segment[0]+1}bp)"
        txt += f"\n{self.feature}\n>"
        return txt