def list_command(args) : log = get_log() e = EnsemblDownloader() suppression_defaults = { 'ensembl' : 70, # errors with 69 and older (missing columns) 'metazoa' : 17, 'protists' : 17, 'plants' : 17, 'bacteria' : 17, 'fungi' : 17, } if not args.suppress : args.suppress = suppression_defaults[args.database] log.info("listing species in %s database" % args.database) log.info("suppressing releases prior to %d" % args.suppress) try : pretty_print_table( ('Species', 'Release'), e.get_all_species(db=args.database, suppress=args.suppress)) except EnsemblDownloadError, ede : log.fatal(ede.message) exit(1)
def list(self) : if not self.params['db_filename'] : print "No reference used..." else : pretty_print_table(('SPECIES','RELEASE','FILENAME','CHECKSUM'), \ [(self.params['db_species'], self.params['db_release'], self.params['db_filename'], self.params['db_checksum'])]) if self.count() == 0 : print "No samples found..." else : pretty_print_table(('SAMPLE','SPECIES','ASSEMBLER','CONTIGS','MD5','BAM','MD5'), \ [ (k, v['species'], v['assembler'], self._abspath(v['contigs']), v['contigs_checksum'], self._abspath(v['bam']), v['bam_checksum']) for k,v in self.params['samples'].iteritems() ])