reader.py 文件源码

def fetch(self, chrom_or_region, begin=None, end=None):
        """Jump to the start position of the given chromosomal position
        and limit iteration to the end position

        :param str chrom_or_region: name of the chromosome to jump to if
            begin and end are given and a samtools region string otherwise
            (e.g. "chr1:123,456-123,900").
        :param int begin: 0-based begin position (inclusive)
        :param int end: 0-based end position (exclusive)
        """
        if begin is not None and end is None:
            raise ValueError('begin and end must both be None or neither')
        # close tabix file if any and is open
        if self.tabix_file and not self.tabix_file.closed:
            self.tabix_file.close()
        # open tabix file if not yet open
        if not self.tabix_file or self.tabix_file.closed:
            self.tabix_file = pysam.TabixFile(
                filename=self.path, index=self.tabix_path)
        # jump to the next position
        if begin is None:
            self.tabix_iter = self.tabix_file.fetch(region=chrom_or_region)
        else:
            self.tabix_iter = self.tabix_file.fetch(
                reference=chrom_or_region, start=begin, end=end)
        return self