ClassSegFeat.py

class Segment:
    def __init__(self,id,feature,chr,start,stop):
        self.id=id
        self.features=feature # list of the features on this segment. if the feature is on the + strand, it will be named '+feature_id', else '-feature_id'

        # position on the original genome
        self.chr=chr
        self.start=start
        self.stop=stop
        
        self.size=self.stop-self.start+1
        
    def __str__(self):
        return f"id={self.id}, position on the original genome={self.chr}:{self.start}-{self.stop}, size={self.size}, features={self.features}"


class Feature:
    def __init__(self,id,type,chr,start,stop,annot,childs,parent,seg_list,strand,complete):
        self.id=id
        self.type=type
        
        # position on the original genome
        self.chr=chr
        self.start=start
        self.stop=stop
        self.strand=strand
        self.size=stop-start+1

        self.pos_start=0 # position on the first segment, setup later
        self.pos_stop=0 # position on the last segment, setup later
        
        self.annot=annot
        self.childs=childs # liste of child features (exons, cds, etc)
        self.parent=parent
        self.segments_list_source=seg_list # list of oriented segments on which the feature is (>s1/<s1, depending on the path of the gene in the graph)
        self.segments_list_target=[] # list of lists, as there can be several occurences of a feature on a given target genome

        self.note="" # from the annotation file
        self.sequence=""

        self.complete=complete # boolean, is the feature initialised with all the info or not

        
    def __str__(self):
        if self.parent=="":
            return f"id={self.id}, type={self.type}, segments={self.segments_list_source}, position on the original genome={self.chr}:{self.start}-{self.stop}, childs={self.childs}, annotation={self.annot}"
        else:
            return f"id={self.id}, type={self.type}, segments={self.segments_list_source}, position on the original genome={self.chr}:{self.start}-{self.stop}, parent={self.parent}, childs={self.childs}, annotation={self.annot}"