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() ])
