atlas.py 文件源码

def download_patric_genomes(self, ids, force_rerun=False):
        """Download genome files from PATRIC given a list of PATRIC genome IDs and load them as strains.

        Args:
            ids (str, list): PATRIC ID or list of PATRIC IDs
            force_rerun (bool): If genome files should be downloaded again even if they exist

        """
        ids = ssbio.utils.force_list(ids)

        counter = 0
        log.info('Downloading sequences from PATRIC...')
        for patric_id in tqdm(ids):
            f = ssbio.databases.patric.download_coding_sequences(patric_id=patric_id, seqtype='protein',
                                                                 outdir=self.sequences_by_organism_dir,
                                                                 force_rerun=force_rerun)
            if f:
                self.load_strain(patric_id, f)
                counter += 1
                log.debug('{}: downloaded sequence'.format(patric_id))
            else:
                log.warning('{}: unable to download sequence'.format(patric_id))

        log.info('Created {} new strain GEM-PROs, accessible at "strains" attribute'.format(counter))