Commit cad75709 authored by Mathieu's avatar Mathieu

Improve the way to deal with augustus species, now it is what the user provides in all cases

parent 7aac31cc
......@@ -2729,7 +2729,7 @@ def _parse_args():
help='Restart an uncompleted run. Not available for the protein mode')
optional.add_argument(
'-sp', '--species', default='generic', required=False, dest='species', metavar='SPECIES',
'-sp', '--species', required=False, dest='species', metavar='SPECIES',
help='Name of existing Augustus species gene finding parameters. '
'See Augustus documentation for available options.')
......@@ -2847,8 +2847,7 @@ def _define_parameters(args):
# Use "generic" as the Augustus species unless user has specified the desired species metaparameters using the
# "-sp species" option
if args['species'] == 'generic':
# in this case, the generic species is fetch in the dataset configuration
if not args['species']:
if not target_species: # 1.x datasets backward compatibility
if clade_name.startswith(('arthrop', 'examp')):
target_species = 'fly'
......@@ -2983,7 +2982,7 @@ def _set_rerun_busco_command(params):
_rerun_cmd += ' --limit %s' % str(params['region_limit'])
if params['tmp'] != './tmp':
_rerun_cmd += ' -t %s' % params['tmp']
if params['target_species'] != Analysis.SPECIES_DEFAULT:
if params['target_species']:
_rerun_cmd += ' -sp %s' % params['target_species']
if params['ev_cutoff'] != Analysis.EVALUE_DEFAULT:
_rerun_cmd += ' -e %s' % str(params['ev_cutoff'])
......
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