reference.py 文件源码

def index_reference(self, in_fasta_fn, in_gtf_fn, num_threads=1, sa_sparse_d=None, sa_index_n_bases=None,
                        chr_bin_n_bits=None, limit_ram=None):
        if os.path.exists(self.reference_star_path):
            raise Exception('STAR reference path %s already exists' % self.reference_star_path)

        os.mkdir(self.reference_star_path)

        args = ['STAR', '--runMode', 'genomeGenerate', '--genomeDir', self.reference_star_path,
                '--runThreadN', str(num_threads), '--genomeFastaFiles', in_fasta_fn,
                '--sjdbGTFfile', in_gtf_fn]
        if limit_ram is not None:
            args += ['--limitGenomeGenerateRAM', str(limit_ram)]
        if sa_sparse_d is not None:
            args += ['--genomeSAsparseD', str(sa_sparse_d)]
        if sa_index_n_bases is not None:
            args += ['--genomeSAindexNbases', str(sa_index_n_bases)]
        if chr_bin_n_bits is not None:
            args += ['--genomeChrBinNbits', str(chr_bin_n_bits)]

        subprocess.check_call(args)