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 _initialise_db(self, species, release, database_name, nucleotide) :
e = EnsemblDownloader()
self.log.info("downloading %s/%d" % (species, release))
try :
self.data = ensembl_to_glutton(e.download(species, release, database_name, nucleotide))
except EnsemblDownloadError, ede :
self.log.fatal(ede.message)
exit(1)
# data is assumed to be a list of tuples
def pretty_print_table(headings, data) :
spacer = 4
num_columns = len(headings)
assert _sanity_check_data(data, num_columns)
headings = [ h.capitalize() for h in headings ]
# generate format string using column widths
fmt = ""
for i in range(num_columns) :
fmt += ("%%-%ds" % (max([len(headings[i])] + [ _safe_len(d[i]) for d in data ]) + spacer))
# print the actual table
s = fmt % tuple(headings)
print ""
print s
print '-'*len(s)
for d in data :
print fmt % tuple(d)
print ""
if __name__ == '__main__' :
from glutton.ensembl_downloader import EnsemblDownloader
e = EnsemblDownloader()
pretty_print_table(['species', 'release'], e.get_all_species('metazoa'))
