reference.py 文件源码

def get_transcript_gc_content(self, transcript_obj):
        pattern = re.compile('[cCgG]')

        gc, length = 0, 0
        for interval in transcript_obj.intervals:
            if interval.chrom not in self.chroms:
                continue

            seq = self.chroms[interval.chrom][interval.start:interval.end]
            gc += len(re.findall(pattern, seq))
            length += interval.length

        if length > 0:
            return float(gc) / float(length)
        else:
            return 0

# NOTE: these stub classes are necessary to maintain backwards compatibility with old refdata (1.2 or older)