def setUp(self):
com1 = Command(
'Summarize Taxa', 'summarize_taxa_through_plots.py',
'{"--otu_table_fp":null}', '{}',
'{"--mapping_category":null, "--mapping_fp":null,'
'"--sort":null}', '{"--output_dir":null}')
com2 = Command(
'Beta Diversity', 'beta_diversity_through_plots.py',
'{"--otu_table_fp":null,"--mapping_fp":null}', '{}',
'{"--tree_fp":null,"--color_by_all_fields":null,'
'"--seqs_per_sample":null}', '{"--output_dir":null}')
com3 = Command(
'Alpha Rarefaction', 'alpha_rarefaction.py',
'{"--otu_table_fp":null,"--mapping_fp":null}', '{}',
'{"--tree_fp":null,"--num_steps":null,'
'"--min_rare_depth"'
':null,"--max_rare_depth":null,'
'"--retain_intermediate_files":false}', '{"--output_dir":null}')
self.all_comms = {
"16S": [com1, com2, com3],
"18S": [com1, com2, com3],
"ITS": [com2, com3],
"Proteomic": [com2, com3],
"Metabolomic": [com2, com3],
"Metagenomic": [com2, com3],
}
def test_get_commands(self):
exp = [
Command('Summarize Taxa', 'summarize_taxa_through_plots.py',
'{"--otu_table_fp":null}', '{}',
'{"--mapping_category":null, "--mapping_fp":null,'
'"--sort":null}', '{"--output_dir":null}'),
Command('Beta Diversity', 'beta_diversity_through_plots.py',
'{"--otu_table_fp":null,"--mapping_fp":null}', '{}',
'{"--tree_fp":null,"--color_by_all_fields":null,'
'"--seqs_per_sample":null}', '{"--output_dir":null}'),
Command('Alpha Rarefaction', 'alpha_rarefaction.py',
'{"--otu_table_fp":null,"--mapping_fp":null}', '{}',
'{"--tree_fp":null,"--num_steps":null,''"--min_rare_depth"'
':null,"--max_rare_depth":null,'
'"--retain_intermediate_files":false}',
'{"--output_dir":null}')
]
self.assertEqual(Job.get_commands(), exp)
