reftools.py 文件源码

def get_chrom_length(self, chrom):
        """
        Extract chromosome length from fasta.

        Parameters
        ----------

        chrom : str
            The name of the chromosome or scaffold.

        Returns
        -------

        length : int
            The length (integer) of the chromsome/scaffold

        Raises
        ------

        RuntimeError
            If chromosome name not present in bam header

        """
        fastafile = pysam.FastaFile(self.filepath)
        lengths = dict(zip(fastafile.references, fastafile.lengths))
        try:
            lens = lengths[chrom]
            fastafile.close()
            return lens
        except:
            self.logger.error(
                "{} not present in {}. Exiting.".format(
                    chrom, self.filepath))
            logging.shutdown()
            raise RuntimeError(
                "Chromosome name not present in fasta. Exiting")