def test_zoo_taxcode(self):
self.taxcode = TaxCode("ZOO")
tests = []
ranks = "Animalia;Chordata;Mammalia;Rodentia;Muridae;Apodemus;agrarius"
expected_levels = "kingdom;phylum;class;order;family;genus;species"
tests += [(ranks, expected_levels)]
ranks = "Animalia;Chordata;Mammalia;Primates;Hominidae;Homininae;Hominini;Hominina;H**o;sapiens"
expected_levels = "kingdom;phylum;class;order;family;subfamily;tribe;subtribe;genus;species"
tests += [(ranks, expected_levels)]
self.check_ranks(tests)
def load_refjson(self, refjson_fname):
try:
self.refjson = RefJsonParser(refjson_fname)
except ValueError:
self.cfg.exit_user_error("ERROR: Invalid json file format!")
#validate input json format
(valid, err) = self.refjson.validate()
if not valid:
self.cfg.log.error(
"ERROR: Parsing reference JSON file failed:\n%s", err)
self.cfg.exit_user_error()
self.rate = self.refjson.get_rate()
self.node_height = self.refjson.get_node_height()
self.origin_taxonomy = self.refjson.get_origin_taxonomy()
self.tax_tree = self.refjson.get_tax_tree()
self.cfg.compress_patterns = self.refjson.get_pattern_compression()
self.bid_taxonomy_map = self.refjson.get_branch_tax_map()
if not self.bid_taxonomy_map:
# old file format (before 1.6), need to rebuild this map from scratch
th = TaxTreeHelper(self.cfg, self.origin_taxonomy)
th.set_mf_rooted_tree(self.tax_tree)
th.set_bf_unrooted_tree(self.refjson.get_reftree())
self.bid_taxonomy_map = th.get_bid_taxonomy_map()
self.write_bid_tax_map(self.bid_taxonomy_map, final=False)
reftree_str = self.refjson.get_raxml_readable_tree()
self.reftree = Tree(reftree_str)
self.reftree_size = len(self.reftree.get_leaves())
# IMPORTANT: set EPA heuristic rate based on tree size!
self.cfg.resolve_auto_settings(self.reftree_size)
# If we're loading the pre-optimized model, we MUST set the same rate het. mode as in the ref file
if self.cfg.epa_load_optmod:
self.cfg.raxml_model = self.refjson.get_ratehet_model()
self.classify_helper = TaxClassifyHelper(self.cfg,
self.bid_taxonomy_map,
self.rate, self.node_height)
self.taxtree_helper = TaxTreeHelper(self.cfg, self.origin_taxonomy,
self.tax_tree)
tax_code_name = self.refjson.get_taxcode()
self.tax_code = TaxCode(tax_code_name)
self.taxonomy = Taxonomy(prefix=EpacConfig.REF_SEQ_PREFIX,
tax_map=self.origin_taxonomy)
self.tax_common_ranks = self.taxonomy.get_common_ranks()
# print "Common ranks: ", self.tax_common_ranks
self.mislabels_cnt = [0] * TaxCode.UNI_TAX_LEVELS
self.rank_mislabels_cnt = [0] * TaxCode.UNI_TAX_LEVELS
def test_bac_taxcode(self):
self.taxcode = TaxCode("BAC")
tests = []
ranks = "Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium;Clostridium rectum"
expected_levels = "kingdom;phylum;class;order;family;genus;species"
tests += [(ranks, expected_levels)]
ranks = "Bacteria;Actinobacteria;Actinobacteria;Actinobacteridae;Actinomycetales;Micrococcineae;Micrococcaceae;Acaricomes;Acaricomes phytoseiuli"
expected_levels = "kingdom;phylum;class;subclass;order;suborder;family;genus;species"
tests += [(ranks, expected_levels)]
ranks = "k__Bacteria; p__Acidobacteria; c__[Chloracidobacteria]; o__[Chloracidobacterales]; f__[Chloracidobacteraceae]; g__Candidatus Chloracidobacterium; s__"
expected_levels = "kingdom;phylum;class;order;family;genus;species"
tests += [(ranks, expected_levels)]
self.check_ranks(tests)
def test_bot_taxcode(self):
self.taxcode = TaxCode("BOT")
tests = []
ranks = "Apocynoideae;Nerieae;Neriinae;Adenium;Adenium_swazicum"
expected_levels = "subfamily;tribe;subtribe;genus;species"
tests += [(ranks, expected_levels)]
ranks = "Apocynoideae;Echiteae;Parsonsiinae;Parsonsia;Parsonsia_heterophylla"
expected_levels = "subfamily;tribe;subtribe;genus;species"
tests += [(ranks, expected_levels)]
# ranks = "Eukaryota;Opisthokonta;Nucletmycea;Fungi;Dikarya;Ascomycota;Saccharomycotina;Saccharomycetes;Saccharomycetales;Metschnikowiaceae;Clavispora;Clavispora lusitaniae ATCC 42720"
ranks = "Eukaryota;Fungi;Dikarya;Ascomycota;Saccharomycotina;Saccharomycetes;Saccharomycetales;Metschnikowiaceae;Clavispora;Clavispora lusitaniae ATCC 42720"
expected_levels = "domain;kingdom;subkingdom;phylum;subphylum;class;order;family;genus;species"
tests += [(ranks, expected_levels)]
self.check_ranks(tests)
